                                                                                 
                                                                                 
                                                                                 
                                                                                 
                   Command Reference for MrBayes ver. 3.2.5                   
                                                                                 
                   (c) John P. Huelsenbeck, Fredrik Ronquist                     
                               and Maxim Teslenko                                
                                                                                 
                                                                                 
   ***************************************************************************   
   *                                                                         *   
   *  1. Command summary                                                     *   
   *                                                                         *   
   ***************************************************************************   
                                                                                 
   ---------------------------------------------------------------------------   
   Commands that are available from the command                                  
   line or from a MrBayes block include:                                         
                                                                                 
   About            -- Describes the program
   Acknowledgments  -- Shows program acknowledgments
   Calibrate        -- Assigns dates to terminals or interior nodes
   Charset          -- Assigns a group of sites to a set
   Charstat         -- Shows status of characters
   Citations        -- Citation of program, models, and methods
   Comparetree      -- Compares the trees from two tree files
   Constraint       -- Defines a constraint on tree topology
   Ctype            -- Assigns ordering for the characters
   Databreaks       -- Defines data breaks for autodiscrete gamma model
   Delete           -- Deletes taxa from the analysis
   Disclaimer       -- Describes program disclaimer
   Exclude          -- Excludes sites from the analysis
   Execute          -- Executes a file
   Help             -- Provides detailed description of commands
   Include          -- Includes sites
   Link             -- Links parameters across character partitions
   Log              -- Logs screen output to a file
   Lset             -- Sets the parameters of the likelihood model
   Manual           -- Prints a command reference to a text file
   Mcmc             -- Starts Markov chain Monte Carlo analysis
   Mcmcp            -- Sets parameters of a chain (without starting analysis)
   Outgroup         -- Changes outgroup taxon
   Pairs            -- Defines nucleotide pairs (doublets) for stem models
   Partition        -- Assigns a character partition
   Plot             -- Plots parameters from MCMC analysis
   Prset            -- Sets the priors for the parameters
   Propset          -- Sets proposal probabilities and tuning parameters
   Quit             -- Quits the program
   Report           -- Controls how model parameters are reported
   Restore          -- Restores taxa
   Set              -- Sets run conditions and defines active data partition
   Showbeagle       -- Show available BEAGLE resources
   Showmatrix       -- Shows current character matrix
   Showmcmctrees    -- Shows trees used in mcmc analysis
   Showmodel        -- Shows model settings
   Showmoves        -- Shows moves for current model
   Showparams       -- Shows parameters in current model
   Showusertrees    -- Shows user-defined trees
   Speciespartition -- Defines a partition of tips into species
   Ss               -- Starts stepping-stone sampling
   Ssp              -- Sets parameters of stepping-stone analysis (without starting)
   Startvals        -- Sets starting values of parameters
   Sump             -- Summarizes parameters from MCMC analysis
   Sumss            -- Summarizes parameters from stepping-stone analysis
   Sumt             -- Summarizes trees from MCMC analysis
   Taxastat         -- Shows status of taxa
   Taxset           -- Assigns a group of taxa to a set
   Unlink           -- Unlinks parameters across character partitions
   Version          -- Shows program version
                                                                                 
   Commands that should be in a NEXUS file (data                                 
   block, trees block or taxa block) include:                                                
                                                                                 
   Begin            -- Denotes beginning of block in file
   Dimensions       -- Defines size of character matrix
   End              -- Denotes end of a block in file
   Endblock         -- Alternative way of denoting end of a block
   Format           -- Defines character format in data block
   Matrix           -- Defines matrix of characters in data block
   Taxlabels        -- Defines taxon labels
   Translate        -- Defines alternative names for taxa
   Tree             -- Defines a tree
                                                                                 
   Note that this program supports the use of the shortest unambiguous           
   spelling of the above commands (e.g., "exe" instead of "execute").        
   ---------------------------------------------------------------------------   
                                                                                 
   ***************************************************************************   
   *                                                                         *   
   *  2. MrBayes commands                                                    *   
   *                                                                         *   
   ***************************************************************************   
                                                                                 
   ---------------------------------------------------------------------------   
   About                                                                         
                                                                                 
   This command provides some general information about the program.             
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Acknowledgments                                                               
                                                                                 
   This command shows the authors' acknowledgments.                              
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Calibrate                                                                     
                                                                                 
   This command dates a terminal or interior node in the tree. The format is     
                                                                                 
      calibrate <node_name> = <age_prior>                                        
                                                                                 
   where <node_name> is the name of a defined interior constraint node or the    
   name of a terminal node (tip) and <age_prior> is a prior probability distribu-
   tion on the age of the node. The latter can either be a fixed date or a date  
   drawn from one of the available prior probability distributions. In general,  
   the available prior probability distributions are parameterized in terms of   
   the expected mean age of the distribution to facilitate for users. Some dis-  
   tributions put a positive probability on all ages above 0.0, while others in- 
   clude a minimum-age constraint and sometimes a maximum-age constraint. The    
   available distributions and their parameters are:                             
                                                                                 
      calibrate <node_name> = fixed(<age>)                                       
      calibrate <node_name> = uniform(<min_age>,<max_age>)                       
      calibrate <node_name> = offsetexponential(<min_age>,<mean_age>)            
      calibrate <node_name> = truncatednormal(<min_age>,<mean_age>,<stdev>)      
      calibrate <node_name> = lognormal(<mean_age>,<stdev>)                      
      calibrate <node_name> = offsetlognormal(<min_age>,<mean_age>,<stdev>)      
      calibrate <node_name> = gamma(<mean_age>,<stdev>)                          
      calibrate <node_name> = offsetgamma(<min_age>,<mean_age>,<stdev>)          
                                                                                 
   Note that mean_age is always the mean age and stdev the standard deviation of 
   the distribution measured in user-defined time units. This way of specifying  
   the distribution parameters is often different from the parameterization used 
   elsewhere in the program. For instance, the standard parameters of the gamma  
   distribution used by MrBayes are shape (alpha) and rate (beta). If you want   
   to use the standard parameterization, the conversions are as follows:         
                                                                                 
      exponential distributon: mean    = 1 / rate                                
      gamma distributon:       mean    = alpha / beta                            
                               st.dev. = square_root (alpha / beta^2)            
      lognormal distributon:   mean    = exp (mean_log + st.dev._log^2/2)        
                               st.dev. = square_root ((exp (st.dev._log^2) - 1)  
                                         * (exp (2*mean_log + st.dev._log^2))    
                                                                                 
   The truncated normal distribution is an exception in that the mean_age and    
   stdev parameters are the mean and standard deviation of the underlying non-   
   truncated normal distribution. The truncation will cause the modified distri- 
   bution to have a higher mean and lower standard deviation. The magnitude of   
   that effect depends on how much of the tail of the distribution is removed.   
                                                                                 
   Note that previous to version 3.2.2, MrBayes used the standard rate parameter-
   ization of the offset exponential. This should not cause a problem in most    
   cases because the old parameterization will result in an error in more recent 
   versions of MrBayes, and the likely source of the error is given in the error 
   message.                                                                      
                                                                                 
   For a practical example, assume that we had three fossil terminals named      
   'FossilA', 'FossilB', and 'FossilC'. Assume further that we want to fix the   
   age of FossilA to 100.0 million years, we think that FossilB is somewhere     
   between 100.0 and 200.0 million years old, and that FossilC is at least 300.0 
   million years old, possibly older but relatively unlikely to be more than     
   400.0 million years old. Then we might use the commands:                      
                                                                                 
      calibrate FossilA = fixed(100) FossilB = uniform(100,200)                  
      calibrate FossilC = offsetexponential(300,400)                             
                                                                                 
   Note that it is possible to give more than one calibration for each           
   'calibrate' statement. Thus, 'calibrate FossilA=<setting> FossilB=<setting>'  
   would be a valid statement.                                                   
                                                                                 
   To actually use the calibrations to obtain dated trees, you also need to set  
   a clock model using relevant 'brlenspr' and 'nodeagepr' options of the 'prset'
   command. You may also want to examine the 'clockvarpr' and 'clockratepr' op-  
   tions. Furthermore, you need to activate the relevant constraint(s) using     
   'topologypr', if you use any dated interior nodes in the tree.                
                                                                                 
   You may wish to remove a calibration from an interior or terminal node, which 
   has previously been calibrated. You can do that using                         
                                                                                 
      calibrate <node_name> = unconstrained                                      
                                                                                 
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Charset                                                                       
                                                                                 
   This command defines a character set. The format for the charset command      
   is                                                                            
                                                                                 
      charset <name> = <character numbers>                                       
                                                                                 
   For example, "charset first_pos = 1-720\3" defines a character set         
   called "first_pos" that includes every third site from 1 to 720.            
   The character set name cannot have any spaces in it. The slash (\)           
   is a nifty way of telling the program to assign every third (or               
   second, or fifth, or whatever) character to the character set.                
   This option is best used not from the command line, but rather as a           
   line in the mrbayes block of a file. Note that you can use "." to           
   stand in for the last character (e.g., charset 1-.\3).                       
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Charstat                                                                      
                                                                                 
   This command shows the status of all the characters. The correct usage        
   is                                                                            
                                                                                 
      charstat                                                                   
                                                                                 
   After typing "charstat", the character number, whether it is excluded       
   or included, and the partition identity are shown. The output is paused       
   every 100 characters. This pause can be turned off by setting autoclose       
   to "yes" (set autoclose=yes).                                               
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Citations                                                                     
                                                                                 
   This command shows a thorough list of citations you may consider using        
   when publishing the results of a MrBayes analysis.                            
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Comparetree                                                                   
                                                                                 
   This command compares the trees in two files, called "filename1" and        
   "filename2". It will output a bivariate plot of the split frequencies       
   as well as plots of the tree distance as a function of the generation. The    
   plots can be used to get a quick indication of whether two runs have con-     
   verged onto the same set of trees. The "Comparetree" command will also      
   produce a ".pairs" file and a ".dists" file (these file endings are added 
   to the end of the "Outputname"). The ".pairs" file contains the paired    
   split frequencies from the two tree samples; the ".dists" file contains the 
   tree distance values.                                                         
                                                                                 
   Note that the "Sumt" command provides a different set of convergence diag-  
   nostics tools that you may also want to explore. Unlike "Comparetree", "Sumt"
   can compare more than two tree samples and will calculate consensus trees and 
   split frequencies from the pooled samples.                                    
                                                                                 
   Options:                                                                      
                                                                                 
   Relburnin     -- If this option is set to 'Yes', then a proportion of the     
                    samples will be discarded as burnin when calculating summary 
                    statistics. The proportion to be discarded is set with       
                    Burninfrac (see below). When the Relburnin option is set to  
                    'No', then a specific number of samples is discarded instead.
                    This number is set by Burnin (see below). Note that the      
                    burnin setting is shared with the 'mcmc', 'sumt', 'sump' and 
                    'plot' commands.                                             
   Burnin        -- Determines the number of samples (not generations) that will 
                    be discarded when summary statistics are calculated. The     
                    value of this option is only relevant when Relburnin is set  
                    to 'No'.                                                     
   BurninFrac    -- Determines the fraction of samples that will be discarded    
                    when summary statistics are calculated. The value of this    
                    option is only relevant when Relburnin is set to 'Yes'.      
                    Example: A value for this option of 0.25 means that 25% of  
                    the samples will be discarded.                               
   Minpartfreq   -- The minimum probability of partitions to include in summary  
                    statistics.                                                  
   Filename1     -- The name of the first tree file to compare.                  
   Filename2     -- The name of the second tree file to compare.                 
   Outputname    -- Name of the file to which 'comparetree' results will be      
                    printed.                                                     
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter       Options                  Current Setting                      
   --------------------------------------------------------                      
   Relburnin       Yes/No                   Yes                                   
   Burnin          <number>                 0                                   
   Burninfrac      <number>                 0.25                               
   Minpartfreq     <number>                 0.00                               
   Filename1       <name>                   temp.t                                   
   Filename2       <name>                   temp.t                                   
   Outputname      <name>                   temp.comp                                   
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Constraint                                                                    
                                                                                 
   This command defines a tree constraint. The format for the constraint         
   command is                                                                    
                                                                                 
      constraint <name> [hard|negative|partial] = <taxon list> [:<taxon list>]   
                                                                                 
   There are three types of constraint implemented in MrBayes. The type of the   
   constraint is specified by using one of the three keywords 'hard', 'negative',
   or 'partial' right after the name of the constraint. If no type is specified, 
   then the constraint is assumed to be 'hard'.                                  
                                                                                 
   In a rooted tree, a 'hard' constraint forces the taxa in the list to form a   
   monophyletic group. In an unrooted tree, the taxon split that separates the   
   taxa in the list from other taxa is forced to be present. The interpretation  
   of this depends on whether the tree is rooted on a taxon outside the list or  
   a taxon in the list. If the outgroup is excluded , the taxa in the list are   
   assumed to form a monophyletic group, but if the outgroup is included, the    
   taxa that are not in the list are forced together.                            
                                                                                 
   A 'negative' constraint bans all the trees that have the listed taxa in the   
   same subtree. In other words, it is the opposite of a hard constraint.        
                                                                                 
   A 'partial' or backbone constraint is defined in terms of two sets of taxa    
   separated by a colon character. The constraint forces all taxa in the first   
   list to form a monophyletic group that does not include any taxon in the      
   second list. Taxa that are not included in either list can be placed in any   
   position on the tree, either inside or outside the constrained group. In an   
   unrooted tree, the two taxon lists can be switched with each other with no    
   effect. For a rooted tree, it is the taxa in the first list that have to be   
   monophyletic, that is, these taxa must share a common ancestor not shared with
   any taxon in the second list. The taxa in the second list may or may not fall 
   in a monophyletic group depending on the rooting of the tree.                 
                                                                                 
   A list of taxa can be specified using a taxset, taxon names, taxon numbers, or
   any combination of the above, sepatated by spaces. The constraint is treated  
   as an absolute requirement of trees, that is, trees that are not compatible   
   with the constraint have zero prior (and hence zero posterior) probabilty.    
                                                                                 
   If you are interested in inferring ancestral states for a particular node,    
   you need to 'hard' constrain that node first using the 'constraint' command.  
   The same applies if you wish to calibrate an interior node in a dated         
   analysis. For more information on how to infer ancestral states, see the help 
   for the 'report' command. For more on dating, see the 'calibrate' command.    
                                                                                 
   It is important to note that simply defining a constraint using this          
   command is not sufficient for the program to actually implement the           
   constraint in an analysis. You must also enforce the constraints using        
   'prset topologypr = constraints (<list of constraints>)'. For more infor-     
   mation on this, see the help on the 'prset' command.                          
                                                                                 
   Examples:                                                                     
                                                                                 
      constraint myclade = Homo Pan Gorilla                                      
                                                                                 
   Defines a hard constraint forcing Homo, Pan, and Gorilla to form a mono-      
   phyletic group or a split that does not include any other taxa.               
                                                                                 
      constraint forbiddenclade negative = Homo Pan Gorilla                      
                                                                                 
   Defines a negative constraint that associates all trees where Homon, Pan, and 
   Gorilla form a monophyletic group with zero posterior probability. In other   
   words, such trees will not be sampled during MCMC.                            
                                                                                 
      constraint backbone partial = Homo Gorilla : Mus                           
                                                                                 
   Defines a partial constraint that keeps Mus outside of the clade defined by   
   the most recent common ancestor of Homo and Gorilla. Other taxa are allowed to
   sit anywhere in the tree. Note that this particular constraint is meaningless 
   in unrooted trees. MrBayes does not assume anything about the position of the 
   outgroup unless it is explicitly included in the partial constraint. Therefore
   a partial constraint must have at least two taxa on each side of the ':' to be
   useful in analyses of unrooted trees. The case is different for rooted trees, 
   where it is sufficient for a partial constraint to have more than one taxon   
   before the ':', as in the example given above, to constrain tree space.       
                                                                                 
   To define a more complex constraint tree, simply combine constraints into a   
   list when issuing the 'prset topologypr' command.                             
                                                                                 
                                                                                
   --------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Ctype                                                                         
                                                                                 
   This command sets the character ordering for standard-type data. The          
   correct usage is:                                                             
                                                                                 
      ctype <ordering>:<characters>                                              
                                                                                 
   The available options for the <ordering> specifier are:                       
                                                                                 
     unordered    -- Movement directly from one state to another is              
                     allowed in an instant of time.                              
     ordered      -- Movement is only allowed between adjacent characters.       
                     For example, perhaps only between 0 <-> 1 and 1 <-> 2       
                     for a three state character ordered as 0 - 1 - 2.           
     irreversible -- Rates of change for losses are 0.                           
                                                                                 
   The characters to which the ordering is applied is specified in manner        
   that is identical to commands such as "include" or "exclude". For         
   example,                                                                      
                                                                                 
      ctype ordered: 10 23 45                                                    
                                                                                 
   defines charactes 10, 23, and 45 to be of type ordered. Similarly,            
                                                                                 
      ctype irreversible: 54 - 67  71-92                                         
                                                                                 
   defines characters 54 to 67 and characters 71 to 92 to be of type             
   irreversible. You can use the "." to denote the last character, and         
   "all" to denote all of the characters. Finally, you can use the             
   specifier "\" to apply the ordering to every n-th character or             
   you can use predefined charsets to specify the character.                     
                                                                                 
   Only one ordering can be used on any specific application of ctype.           
   If you want to apply different orderings to different characters, then        
   you need to use ctype multiple times. For example,                            
                                                                                 
      ctype ordered: 1-50                                                        
      ctype irreversible: 51-100                                                 
                                                                                 
   sets characters 1 to 50 to be ordered and characters 51 to 100 to be          
   irreversible.                                                                 
                                                                                 
   The ctype command is only sensible with morphological (here called            
   "standard") characters. The program ignores attempts to apply char-         
   acter orderings to other types of characters, such as DNA characters.         
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Databreaks                                                                    
                                                                                 
   This command is used to specify breaks in your input data matrix. Your        
   data may be a mixture of genes or a mixture of different types of data.       
   Some of the models implemented by MrBayes account for nonindependence at      
   adjacent characters. The autocorrelated gamma model, for example, allows      
   rates at adjacent sites to be correlated. However, there is no way for        
   such a model to tell whether two sites, adjacent in the matrix, are           
   actually separated by many kilobases or megabases in the genome. The          
   databreaks command allows you to specify such breaks. The correct             
   usage is:                                                                     
                                                                                 
      databreaks <break 1> <break 2> <break 3> ...                               
                                                                                 
   For example, say you have a data matrix of 3204 characters that include       
   nucleotide data from three genes. The first gene covers characters 1 to       
   970, the second gene covers characters 971 to 2567, and the third gene        
   covers characters 2568 to 3204. Also, let's assume that the genes are         
   not directly adjacent to one another in the genome, as might be likely        
   if you have mitochondrial sequences. In this case, you can specify            
   breaks between the genes using:                                               
                                                                                 
      databreaks 970 2567;                                                       
                                                                                 
   The first break, between genes one and two, is after character 970 and        
   the second break, between genes two and three, is after character 2567.       
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Delete                                                                        
                                                                                 
   This command deletes taxa from the analysis. The correct usage is:            
                                                                                 
      delete <name and/or number and/or taxset> ...                              
                                                                                 
   A list of the taxon names or taxon numbers (labelled 1 to ntax in the order   
   in the matrix) or taxset(s) can be used.  For example, the following:         
                                                                                 
      delete 1 2 Homo_sapiens                                                    
                                                                                 
   deletes taxa 1, 2, and the taxon labelled Homo_sapiens from the analysis.     
   You can also use "all" to delete all of the taxa. For example,              
                                                                                 
      delete all                                                                 
                                                                                 
   deletes all of the taxa from the analysis. Of course, a phylogenetic anal-    
   ysis that does not include any taxa is fairly uninteresting.                  
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Disclaimer                                                                    
                                                                                 
   This command shows the disclaimer for the program. In short, the disclaimer   
   states that the authors are not responsible for any silly things you may do   
   to your computer or any unforseen but possibly nasty things the computer      
   program may inadvertently do to you.                                          
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Exclude                                                                       
                                                                                 
   This command excludes characters from the analysis. The correct usage is      
                                                                                 
      exclude <number> <number> <number>                                         
                                                                                 
   or                                                                            
                                                                                 
      exclude <number> - <number>                                                
                                                                                 
   or                                                                            
                                                                                 
      exclude <charset>                                                          
                                                                                 
   or some combination thereof. Moreover, you can use the specifier "\" to    
   exclude every nth character. For example, the following                       
                                                                                 
      exclude 1-100\3                                                           
                                                                                 
   would exclude every third character. As a specific example,                   
                                                                                 
      exclude 2 3 10-14 22                                                       
                                                                                 
   excludes sites 2, 3, 10, 11, 12, 13, 14, and 22 from the analysis. Also,      
                                                                                 
      exclude all                                                                
                                                                                 
   excludes all of the characters from the analysis. Excluding all characters    
   does not leave you much information for inferring phylogeny.                  
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Execute                                                                       
                                                                                 
   This command executes a file called <file name>. The correct usage is:        
                                                                                 
      execute <file name>                                                        
                                                                                 
   For example,                                                                  
                                                                                 
      execute replicase.nex                                                      
                                                                                 
   would execute the file named "replicase.nex". This file must be in the      
   same directory as the executable.                                             
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Help                                                                          
                                                                                 
   This command provides useful information on the use of this program. The      
   correct usage is                                                              
                                                                                 
      help                                                                       
                                                                                 
   which gives a list of all available commands with a brief description of      
   each or                                                                       
                                                                                 
      help <command>                                                             
                                                                                 
   which gives detailed information on the use of <command>.                     
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Include                                                                       
                                                                                 
   This command includes characters that were previously excluded from the       
   analysis. The correct usage is                                                
                                                                                 
      include <number> <number> <number>                                         
                                                                                 
   or                                                                            
                                                                                 
      include <number> - <number>                                                
                                                                                 
   or                                                                            
                                                                                 
      include <charset>                                                          
                                                                                 
   or some combination thereof. Moreover, you can use the specifier "\" to    
   include every nth character. For example, the following                       
                                                                                 
      include 1-100\3                                                           
                                                                                 
   would include every third character. As a specific example,                   
                                                                                 
      include 2 3 10-14 22                                                       
                                                                                 
   includes sites 2, 3, 10, 11, 12, 13, 14, and 22 from the analysis. Also,      
                                                                                 
      include all                                                                
                                                                                 
   includes all of the characters in the analysis. Including all of the          
   characters (even if many of them are bad) is a very total-evidence-like       
   thing to do. Doing this will make a certain group of people very happy.       
   On the other hand, simply using this program would make those same people     
   unhappy.                                                                      
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Link                                                                          
                                                                                 
   This command links model parameters across partitions of the data. The        
   correct usage is:                                                             
                                                                                 
      link <parameter name> = (<all> or <partition list>)                        
                                                                                 
   The list of parameters that can be linked includes:                           
                                                                                 
      Tratio          -- Transition/transversion rate ratio                      
      Revmat          -- Substitution rates of GTR model                         
      Omega           -- Nonsynonymous/synonymous rate ratio                     
      Statefreq       -- Character state frequencies                             
      Shape           -- Gamma/LNorm shape parameter                             
      Pinvar          -- Proportion of invariable sites                          
      Correlation     -- Correlation parameter of autodiscrete gamma             
      Ratemultiplier  -- Rate multiplier for partitions                          
      Switchrates     -- Switching rates for covarion model                      
      Topology        -- Topology of tree                                        
      Brlens          -- Branch lengths of tree                                  
      Speciationrate  -- Speciation rates for birth-death process                
      Extinctionrate  -- Extinction rates for birth-death process                
      Popsize         -- Population size for coalescence process                 
      Growthrate      -- Growth rate of coalescence process                      
      Aamodel         -- Aminoacid rate matrix                                   
      Cpprate         -- Rate of Compound Poisson Process (CPP)                  
      Cppmultdev      -- Standard dev. of CPP rate multipliers (log scale)       
      Cppevents       -- CPP events                                              
      TK02var         -- Variance increase in TK02 relaxed clock model           
      Igrvar          -- Variance increase in IGR relaxed clock model            
      Mixedvar        -- Variance increase in Mixed relaxed clock model          
                                                                                 
   For example,                                                                  
                                                                                 
      link shape=(all)                                                           
                                                                                 
   links the gamma/lnorm shape parameter across all partitions of the data.      
   You can use "showmodel" to see the current linking status of the            
   characters. For more information on this command, see the help menu           
   for link's converse, unlink ("help unlink");                                
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Log                                                                           
                                                                                 
   This command allows output to the screen to also be output to a file.         
   The useage is:                                                                
                                                                                 
      log start/stop filename=<name> append/replace                              
                                                                                 
   The options are:                                                              
                                                                                 
   Start/Stop     -- Starts or stops logging of output to file.                  
   Append/Replace -- Either append to or replace existing file.                  
   Filename       -- Name of log file (currently, the name of the log            
                     file is "log.out").
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Lset                                                                          
                                                                                 
   This command sets the parameters of the likelihood model. The likelihood      
   function is the probability of observing the data conditional on the phylo-   
   genetic model. In order to calculate the likelihood, you must assume a        
   model of character change. This command lets you tailor the biological        
   assumptions made in the phylogenetic model. The correct usage is              
                                                                                 
      lset <parameter>=<option> ... <parameter>=<option>                         
                                                                                 
   For example, "lset nst=6 rates=gamma" would set the model to a general      
   model of DNA substition (the GTR) with gamma-distributed rate variation       
   across sites.                                                                 
                                                                                 
   Options:                                                                      
                                                                                 
   Applyto   -- This option allows you to apply the lset commands to specific    
                partitions. This command should be the first in the list of      
                commands specified in lset. Moreover, it only makes sense to     
                be using this command if the data have been partitioned. A       
                default partition is set on execution of a matrix. If the data   
                are homogeneous (i.e., all of the same data type), then this     
                partition will not subdivide the characters. Up to 30 other      
                partitions can be defined, and you can switch among them using   
                "set partition=<partition name>". Now, you may want to         
                specify different models to different partitions of the data.    
                Applyto allows you to do this. For example, say you have         
                partitioned the data by codon position, and you want to apply    
                a nst=2 model to the first two partitions and nst=6 to the       
                last. This could be implemented in two uses of lset:             
                                                                                 
                   lset applyto=(1,2) nst=2                                      
                                                                                 
                   lset applyto=(3) nst=6                                        
                                                                                 
                The first applies the parameters after "applyto" to the        
                first and second partitions. The second lset applies nst=6       
                to the third partition. You can also use applyto=(all), which    
                attempts to apply the parameter settings to all of the data      
                partitions. Importantly, if the option is not consistent with    
                the data in the partition, the program will not apply the        
                lset option to that partition.                                   
   Nucmodel  -- This specifies the general form of the nucleotide substitution   
                model. The options are "4by4" [the standard model of DNA       
                substitution in which there are only four states (A,C,G,T/U)],   
                "doublet" (a model appropriate for modelling the stem regions  
                of ribosomal genes where the state space is the 16 doublets of   
                nucleotides), "codon" (the substitution model is expanded      
                around triplets of nucleotides--a codon), and "Protein"        
                (triplets of nucleotides are translated to amino acids, which    
                form the basis of the substitution model).                       
   Nst       -- Sets the number of substitution types: "1" constrains all of   
                the rates to be the same (e.g., a JC69 or F81 model); "2" all- 
                ows transitions and transversions to have potentially different  
                rates (e.g., a K80 or HKY85 model); "6" allows all rates to    
                be different, subject to the constraint of time-reversibility    
                (e.g., a GTR model). Finally, 'nst' can be set to 'mixed', which 
                results in the Markov chain sampling over the space of all poss- 
                ible reversible substitution models, including the GTR model and 
                all models that can be derived from it model by grouping the six 
                rates in various combinations. This includes all the named models
                above and a large number of others, with or without name.        
   Code      -- Enforces the use of a particular genetic code. The default       
                is the universal code. Other options include "vertmt" for      
                vertebrate mitocondrial DNA, "mycoplasma", "yeast",          
                "ciliates", and "metmt" (for metazoan mitochondrial DNA      
                except vertebrates).                                             
   Ploidy    -- Specifies the ploidy of the organism. Options are "Haploid",   
                "Diploid" or "Zlinked". This option is used when a coalescent
                prior is used on trees.                                          
   Rates     -- Sets the model for among-site rate variation. In general, the    
                rate at a site is considered to be an unknown random variable.   
                The valid options are:                                           
                * equal    -- No rate variation across sites.                    
                * gamma    -- Gamma-distributed rates across sites. The rate     
                              at a site is drawn from a gamma distribution.      
                              The gamma distribution has a single parameter      
                              that describes how much rates vary.                
                * lnorm    -- Log Normal-distributed rates across sites. The     
                              rate at a site is drawn from a lognormal           
                              distribution. the lognormal distribiton has a      
                              single parameter, sigma (SD) that describes how    
                              much rates vary (mean fixed to log(1.0) == 0.0.    
                * adgamma  -- Autocorrelated rates across sites. The marg-       
                              inal rate distribution is gamma, but adjacent      
                              sites have correlated rates.                       
                * propinv  -- A proportion of the sites are invariable.          
                * invgamma -- A proportion of the sites are invariable while     
                              the rate for the remaining sites are drawn from    
                              a gamma distribution.                              
                Note that MrBayes versions 2.0 and earlier supported options     
                that allowed site specific rates (e.g., ssgamma). In versions    
                3.0 and later, site specific rates are allowed, but set using    
                the 'prset ratepr' command for each partition.                   
   Ngammacat -- Sets the number of rate categories for the gamma distribution.   
                The gamma distribution is continuous. However, it is virtually   
                impossible to calculate likelihoods under the continuous gamma   
                distribution. Hence, an approximation to the continuous gamma    
                is used; the gamma distribution is broken into ncat categories   
                of equal weight (1/ncat). The mean rate for each category rep-   
                resents the rate for the entire cateogry. This option allows     
                you to specify how many rate categories to use when approx-      
                imating the gamma. The approximation is better as ncat is inc-   
                reased. In practice, "ncat=4" does a reasonable job of         
                approximating the continuous gamma.                              
                It is also used to set the number of rate categories for the     
                lognormal distribution to avoid changing too much of the code,   
                although the name is bad (should add Nlnormcat in future).       
   Nbetacat  -- Sets the number of rate categories for the beta distribution.    
                A symmetric beta distribution is used to model the stationary    
                frequencies when morphological data are used. This option        
                specifies how well the beta distribution will be approximated.   
   Omegavar  -- Allows the nonsynonymous/synonymous rate ratio (omega) to vary   
                across codons. Ny98 assumes that there are three classes, with   
                potentially different omega values (omega1, omega2, omega3):     
                omega2 = 1; 0 < omega1 < 1; and omega3 > 1. Like the Ny98 model, 
                the M3 model has three omega classes. However, their values are  
                less constrained, with omega1 < omega2 < omega3. The default     
                (omegavar = equal) has no variation on omega across sites.       
   Covarion  -- This forces the use of a covarion-like model of substitution     
                for nucleotide or amino acid data. The valid options are "yes" 
                and "no". The covarion model allows the rate at a site to      
                change over its evolutionary history. Specifically, the site     
                is either on or off. When it is off, no substitutions are poss-  
                ible. When the process is on, substitutions occur according to   
                a specified substitution model (specified using the other        
                lset options).                                                   
   Coding    -- This specifies how characters were sampled. If all site patterns 
                had the possibility of being sampled, then "all" should be     
                specified (the default). Otherwise "variable" (only variable   
                characters had the possibility of being sampled), "noabsence"  
                (characters for which all taxa were coded as absent were not     
                sampled), and "nopresence" (characters for which all taxa were 
                coded as present were not sampled. "All" works for all data    
                types. However, the others only work for morphological (all/     
                variable) or restriction site (all/variable/noabsence/nopresence)
                data.                                                            
   Parsmodel -- This forces calculation under the so-called parsimony model      
                described by Tuffley and Steel (1998). The options are "yes"   
                or "no". Note that the biological assumptions of this model    
                are anything but parsimonious. In fact, this model assumes many  
                more parameters than the next most complicated model implemented 
                in this program. If you really believe that the parsimony model  
                makes the biological assumptions described by Tuffley and Steel, 
                then the parsimony method is miss-named.                         
                                                                                 
   Default model settings:                                                       
                                                                                 
   Parameter    Options                               Current Setting            
   ------------------------------------------------------------------            
   Nucmodel     4by4/Doublet/Codon/Protein            4by4                         
   Nst          1/2/6/Mixed                           1                         
   Code         Universal/Vertmt/Mycoplasma/                                     
                Yeast/Ciliates/Metmt                  Universal                         
   Ploidy       Haploid/Diploid/Zlinked               Diploid                         
   Rates        Equal/Gamma/LNorm/Propinv/                                       
                Invgamma/Adgamma                      Equal                         
   Ngammacat    <number>                              4                         
   Nbetacat     <number>                              5                         
   Omegavar     Equal/Ny98/M3                         Equal                         
   Covarion     No/Yes                                No                         
   Coding       All/Variable/Noabsencesites/                                     
                Nopresencesites                       All                         
   Parsmodel    No/Yes                                No                         
   ------------------------------------------------------------------            
                                                                                 
   ---------------------------------------------------------------------------   
   Manual                                                                        
                                                                                 
   This command allows you to generate a text file containing help information   
   on all the available commands. This text file can be used as an up-to-date    
   command reference. You can set the name of the text file using the            
   "filename" option; the default is "commref_mb<version>.txt".              
                                                                                 
   Parameter       Options                  Current Setting                      
   --------------------------------------------------------                      
   Filename        <name>                   commref_mb3.2.5-svn.txt                                   
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Mcmc                                                                          
                                                                                 
   This command starts the Markov chain Monte Carlo (MCMC) analysis. The         
   posterior probability of phylogenetic trees (and other parameters of the      
   substitution model) cannot be determined analytically. Instead, MCMC is       
   used to approximate the posterior probabilities of trees by drawing           
   (dependent) samples from the posterior distribution. This program can         
   implement a variant of MCMC called "Metropolis-coupled Markov chain Monte    
   Carlo", or MCMCMC for short. Basically, "Nchains" are run, with            
   Nchains - 1 of them heated. The chains are labelled 1, 2, ..., Nchains.       
   The heat that is applied to the i-th chain is B = 1 / (1 + temp X i). B       
   is the power to which the posterior probability is raised. When B = 0, all    
   trees have equal probability and the chain freely visits trees. B = 1 is      
   the "cold" chain (or the distribution of interest). MCMCMC can mix          
   better than ordinary MCMC; after all of the chains have gone through          
   one cycle, two chains are chosen at random and an attempt is made to          
   swap the states (with the probability of a swap being determined by the       
   Metropolis et al. equation). This allows the chain to potentially jump        
   a valley in a single bound. The correct usage is                              
                                                                                 
      mcmc <parameter> = <value> ... <parameter> = <value>                       
                                                                                 
   For example,                                                                  
                                                                                 
      mcmc ngen=100000 nchains=4 temp=0.5                                        
                                                                                 
   performs a MCMCMC analysis with four chains with the temperature set to       
   0.5. The chains would be run for 100,000 cycles.                              
                                                                                 
   Options:                                                                      
                                                                                 
   Ngen         -- This option sets the number of cycles for the MCMC alg-       
                   orithm. This should be a big number as you want the chain     
                   to first reach stationarity, and then remain there for        
                   enough time to take lots of samples.                          
   Nruns        -- How many independent analyses are started simultaneously.     
   Nchains      -- How many chains are run for each analysis for the MCMCMC      
                   variant. The default is 4: 1 cold chain and 3 heated chains.  
                   If Nchains is set to 1, MrBayes will use regular MCMC sam-    
                   pling, without heating.                                       
   Temp         -- The temperature parameter for heating the chains. The higher  
                   the temperature, the more likely the heated chains are to     
                   move between isolated peaks in the posterior distribution.    
                   However, excessive heating may lead to very low acceptance    
                   rates for swaps between different chains. Before changing the 
                   default setting, however, note that the acceptance rates of   
                   swaps tend to fluctuate during the burn-in phase of the run.  
   Reweight     -- Here, you specify three numbers, that respectively represent  
                   the percentage of characters to decrease in weight, the       
                   percentage of characters to increase in weight, and the       
                   increment. An increase/decrease in weight is acheived by      
                   replicating/removing a character in the matrix. This is       
                   only done to non-cold chains. The format for this parameter   
                   is "reweight=(<number>,<number>)" or "reweight=(<number>,  
                   <number>,<number>)".                                         
   Swapfreq     -- This specifies how often swaps of states between chains are   
                   attempted. You must be running at least two chains for this   
                   option to be relevant. The default is Swapfreq=1, resulting   
                   in Nswaps (see below) swaps being tried each generation of    
                   the run. If Swapfreq is set to 10, then Nswaps swaps will be  
                   tried every tenth generation of the run.                      
   Nswaps       -- The number of swaps tried for each swapping generation of the 
                   chain (see also Swapfreq).                                    
   Samplefreq   -- This specifies how often the Markov chain is sampled. You     
                   can sample the chain every cycle, but this results in very    
                   large output files. Thinning the chain is a way of making     
                   these files smaller and making the samples more independent.  
   Printfreq    -- This specifies how often information about the chain is       
                   printed to the screen.                                        
   Printall     -- If set to NO, only cold chains in a MCMC analysis are printed 
                   to screen. If set to YES, both cold and heated chains will be 
                   output. This setting only affects the printing to screen, it  
                   does not change the way values are written to file.           
   Printmax     -- The maximum number of chains to print to screen.              
   Mcmcdiagn    -- Determines whether acceptance ratios of moves and swaps will  
                   be printed to file. The file will be named similarly to the   
                   '.p' and '.t' files, but will have the ending '.mcmc'. If     
                   more than one independent analysis is run simultaneously (see 
                   Nruns below), convergence diagnostics for tree topology will  
                   also be printed to this file. The convergence diagnostic used 
                   is the average standard deviation in partition frequency      
                   values across independent analyses. The Burnin setting (see   
                   below) determines how many samples will be discarded as burnin
                   before calculating the partition frequencies. The Minpartfreq 
                   setting (see below) determines the minimum partition frequency
                   required for a partition to be included in the calculation. As
                   the independent analyses approach stationarity (converge), the
                   value of the diagnostic is expected to approach zero.         
   Diagnfreq    -- The number of generations between the calculation of MCMC     
                   diagnostics (see Mcmcdiagn above).                            
   Diagnstat    -- The statistic to use for run-time convergence diagnostics.    
                   Choices are 'Avgstddev' for average standard deviation of     
                   split frequencies and 'Maxstddev' for maximum standard devia- 
                   tion of split frequencies.                                    
   Savetrees    -- If you are using a relative burnin for run-time convergence   
                   diagnostics, tree samples need to be deleted from split       
                   frequency counters as the cut-off point for the burnin moves  
                   during the run. If 'Savetrees' is set to 'No', tree samples   
                   to be discarded are read back in from file. If 'Savetrees' is 
                   set to 'Yes', the tree samples to be removed will be stored   
                   in the internal memory instead. This can use up a lot of      
                   memory in large analyses.                                     
   Minpartfreq  -- The minimum frequency required for a partition to be included 
                   in the calculation of the topology convergence diagnostic. The
                   partition is included if the minimum frequency is reached in  
                   at least one of the independent tree samples that are com-    
                   pared.                                                        
   Allchains    -- If this option is set to YES, acceptance ratios for moves are 
                   recorded for all chains, cold or heated. By default, only the 
                   acceptance ratios for the cold chain are recorded.            
   Allcomps     -- If this option is set to YES, topological convergence diag-   
                   nostics are calculated over all pairwise comparisons of runs. 
                   If it is set to NO, only the overall value is reported.       
   Relburnin    -- If this option is set to YES, then a proportion of the sampled
                   values will be discarded as burnin when calculating the con-  
                   vergence diagnostic. The proportion to be discarded is set    
                   with Burninfrac (see below). When the Relburnin option is set 
                   to NO, then a specific number of samples will be discarded    
                   instead. This number is set by Burnin (see below).            
   Burnin       -- Determines the number of samples (not generations) that will  
                   be discarded when convergence diagnostics are calculated.     
                   The value of this option is only relevant when Relburnin is   
                   set to NO.                                                    
   BurninFrac   -- Determines the fraction of samples that will be discarded     
                   when convergence diagnostics are calculated. The value of     
                   this option is only relevant when Relburnin is set to YES.    
                   Example: A value for this option of 0.25 means that 25% of   
                   the samples will be discarded.                                
   Stoprule     -- If this option is set to NO, then the chain is run the number 
                   of generations determined by Ngen. If it is set to YES, and   
                   topological convergence diagnostics are calculated (Mcmcdiagn 
                   is set to YES), then the chain will be stopped before the pre-
                   determined number of generations if the convergence diagnostic
                   falls below the stop value.                                   
   Stopval      -- The critical value for the topological convergence diagnostic.
                   Only used when Stoprule and Mcmcdiagn are set to yes, and     
                   more than one analysis is run simultaneously (Nruns > 1).     
   Checkpoint   -- If this parameter is set to 'Yes', all the current parameter  
                   values of all chains will be printed to a check-pointing file 
                   every 'Checkfreq' generation of the analysis. The file will be
                   named <Filename>.ckp and allows you to restart the analysis   
                   from the last check point. This can be handy if you are       
                   running a long analysis and want to extend it, or if there is 
                   a risk that a long analysis will be inadvertently interupted  
                   by hardware failure or other factors that are out of your     
                   control.                                                      
   Checkfreq    -- The number of generations between check-pointing. See the     
                   'Checkpoint' parameter above for more information.            
   Filename     -- The name of the files that will be generated. Two files       
                   are generated: "<Filename>.t" and "<Filename>.p".         
                   The .t file contains the trees whereas the .p file con-       
                   tains the sampled values of the parameters.                   
   Startparams  -- The starting values for the model parameters are set to       
                   arbitrary or random values when the parameters are created.   
                   These starting values can be altered using the 'Startvals'    
                   command. The 'Startparams=reset' option allows you to reset   
                   the starting values to the default at the start of the ana-   
                   lysis, overriding any previous user-defined starting values.  
                   Under the default option, 'current', the chains will use the  
                   current starting values.                                      
   Starttree    -- The starting tree(s) for the chain can either be randomly     
                   selected or user-defined. It might be a good idea to          
                   start from randomly chosen trees; convergence seems           
                   likely if independently run chains, each of which             
                   started from different random trees, converge to the same     
                   answer. If you want the chain to start from user-defined      
                   trees instead, you first need to read in your tree(s) from a  
                   Nexus file with a 'trees' block, and then you need to set the 
                   starting tree(s) using the 'Startvals' command. Finally, you  
                   need to make sure that 'Starttree' is set to 'current'. If    
                   you do not set the starting tree(s), the chains will start    
                   with random trees. Setting 'Starttree' to 'random' causes     
                   new starting trees to be drawn randomly at the start of the   
                   run, overwriting any previous user-defined starting trees.    
   Nperts       -- This is the number of random perturbations to apply to the    
                   user starting tree. This allows you to have something         
                   between completely random and user-defined trees start        
                   the chain.                                                    
   Data         -- When Data is set to NO, the chain is run without data. This   
                   should be used only for examining induced priors. DO NOT SET  
                   'DATA' TO 'NO' UNLESS YOU KNOW WHAT YOU ARE DOING!            
   Ordertaxa    -- Determines whether taxa should be ordered before trees are    
                   printed to file. If set to 'Yes', terminals in the sampled    
                   trees will be reordered to match the order of the taxa in the 
                   data matrix as closely as possible. By default, trees will be 
                   printed without reordering of taxa.                           
   Append       -- Set this to 'Yes' to append the results of the current run to 
                   a previous run. MrBayes will first read in the results of the 
                   previous run (number of generations and sampled splits) and   
                   will then continue that run where you left it off. Make sure  
                   that the output file names used in the previous run are the   
                   same as those in the current run.                             
   Autotune     -- Set this to 'Yes' to autotune the proposals that change       
                   substitution model parameters. When set to 'No', the tuning   
                   parameters are fixed to their starting values. Note that the  
                   autotuning occurs independently for each chain. The target    
                   acceptance rate for each move can be changed using the        
                   'Propset' command.                                            
   Tunefreq     -- When a proposal has been tried 'Tunefreq' times, its tuning   
                   parameter is adjusted to reach the target acceptance rate     
                   if 'Autotune' is set to 'Yes'.                                
                                                                                 
   Parameter       Options               Current Setting                         
   -----------------------------------------------------                         
   Ngen            <number>              1000000                                      
   Nruns           <number>              2                                      
   Nchains         <number>              4                                      
   Temp            <number>              0.100000                                     
   Reweight        <number>,<number>     0.00 v 0.00 ^                       
   Swapfreq        <number>              1                                      
   Nswaps          <number>              1                                      
   Samplefreq      <number>              500                                      
   Printfreq       <number>              1000                                      
   Printall        Yes/No                Yes                                      
   Printmax        <number>              8                                      
   Mcmcdiagn       Yes/No                Yes                                      
   Diagnfreq       <number>              5000                                      
   Diagnstat       Avgstddev/Maxstddev   Avgstddev                                     
   Minpartfreq     <number>              0.10                                 
   Allchains       Yes/No                No                                     
   Allcomps        Yes/No                No                                     
   Relburnin       Yes/No                Yes                                     
   Burnin          <number>              0                                     
   Burninfrac      <number>              0.25                                 
   Stoprule        Yes/No                No                                     
   Stopval         <number>              0.05                                 
   Savetrees       Yes/No                No                                     
   Checkpoint      Yes/No                Yes                                     
   Checkfreq       <number>              2000                                     
   Filename        <name>                temp.<p/t>
   Startparams     Current/Reset         Current                                     
   Starttree       Current/Random/       Current                                     
                   Parsimony                                                    
   Nperts          <number>              0                                     
   Data            Yes/No                Yes                                     
   Ordertaxa       Yes/No                No                                     
   Append          Yes/No                No                                     
   Autotune        Yes/No                Yes                                     
   Tunefreq        <number>              100                                     
                                                                                
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Mcmcp                                                                         
                                                                                 
   This command sets the parameters of the Markov chain Monte Carlo (MCMC)       
   analysis without actually starting the chain. This command is identical       
   in all respects to Mcmc, except that the analysis will not start after        
   this command is issued. For more details on the options, check the help       
   menu for Mcmc.
                                                                                 
   Parameter       Options               Current Setting                         
   -----------------------------------------------------                         
   Ngen            <number>              1000000                                      
   Nruns           <number>              2                                      
   Nchains         <number>              4                                      
   Temp            <number>              0.100000                                     
   Reweight        <number>,<number>     0.00 v 0.00 ^                       
   Swapfreq        <number>              1                                      
   Nswaps          <number>              1                                      
   Samplefreq      <number>              500                                      
   Printfreq       <number>              1000                                      
   Printall        Yes/No                Yes                                      
   Printmax        <number>              8                                      
   Mcmcdiagn       Yes/No                Yes                                      
   Diagnfreq       <number>              5000                                      
   Diagnstat       Avgstddev/Maxstddev   Avgstddev                                     
   Minpartfreq     <number>              0.10                                 
   Allchains       Yes/No                No                                     
   Allcomps        Yes/No                No                                     
   Relburnin       Yes/No                Yes                                     
   Burnin          <number>              0                                     
   Burninfrac      <number>              0.25                                 
   Stoprule        Yes/No                No                                     
   Stopval         <number>              0.05                                 
   Savetrees       Yes/No                No                                     
   Checkpoint      Yes/No                Yes                                     
   Checkfreq       <number>              2000                                     
   Filename        <name>                temp.<p/t>
   Startparams     Current/Reset         Current                                     
   Starttree       Current/Random/       Current                                     
                   Parsimony                                                    
   Nperts          <number>              0                                     
   Data            Yes/No                Yes                                     
   Ordertaxa       Yes/No                No                                     
   Append          Yes/No                No                                     
   Autotune        Yes/No                Yes                                     
   Tunefreq        <number>              100                                     
                                                                                
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Outgroup                                                                      
                                                                                 
   This command assigns a taxon to the outgroup. The correct usage is:           
                                                                                 
      outgroup <number>/<taxon name>                                             
                                                                                 
   For example, "outgroup 3" assigns the third taxon in the matrix to be       
   the outgroup. Similarly, "outgroup Homo_sapiens" assings the taxon          
   "Homo_sapiens" to be the outgroup (assuming that there is a taxon named     
   "Homo_sapiens" in the matrix). Only a single taxon can be assigned to       
   be the outgroup.                                                              
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Pairs                                                                         
                                                                                 
   This command is used to specify pairs of nucleotides. For example, your       
   data may be RNA sequences with a known secondary structure of stems and       
   loops. Substitutions in nucleotides involved in a Watson-Crick pairing        
   in stems are not strictly independent; a change in one changes the prob-      
   ability of a change in the partner. A solution to this problem is to          
   expand the model around the pair of nucleotides in the stem. This             
   command allows you to do this. The correct usage is:                          
                                                                                 
      pairs <NUC1>:<NUC2>, <NUC1>:<NUC2>,..., <NUC1>:<NUC2>;                     
                                                                                 
   For example,                                                                  
                                                                                 
      pairs 30:56, 31:55, 32:54, 33:53, 34:52, 35:51, 36:50;                     
                                                                                 
   specifies pairings between nucleotides 30 and 56, 31 and 55, etc. Only        
   nucleotide data (DNA or RNA) may be paired using this command. Note that      
   in order for the program to actually implement a "doublet" model            
   involving a 16 X 16 rate matrix, you must specify that the structure of       
   the model is 16 X 16 using "lset nucmodel=doublet".                         
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Partition                                                                     
                                                                                 
   This command allows you to specify a character partition. The format for      
   this command is                                                               
                                                                                 
      partition <name> = <num parts>:<chars in first>, ...,<chars in last>       
                                                                                 
   For example, "partition by_codon = 3:1st_pos,2nd_pos,3rd_pos" specifies     
   a partition called "by_codon" which consists of three parts (first,         
   second, and third codon positions). Here, we are assuming that the sites      
   in each partition were defined using the charset command. You can specify     
   a partition without using charset as follows:                                 
                                                                                 
      partition by_codon = 3:1 4 6 9 12,2 5 7 10 13,3 6 8 11 14                  
                                                                                 
   However, we recommend that you use the charsets to define a set of char-      
   acters and then use these predefined sets when defining the partition.        
   Also, it makes more sense to define a partition as a line in the mrbayes      
   block than to issue the command from the command line (then again, you        
   may be a masochist, and want to do extra work).                               
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Plot                                                                          
                                                                                 
   This command plots specified parameters in the .p file or one of the .p files 
   created during an MCMC analysis. An x-y graph of the parameter over the course
   of the chain is created. The command can be useful for visually diagnosing    
   convergence for many of the parameters of the phylogenetic model. The para-   
   meter to be plotted is specified by the "parameter" option. Several para-   
   meters can be plotted at once by using the "match" option, which has a      
   default value of "perfect". For example, if you were to set "parameter = pi"
   and "match = consistentwith", then all of the state frequency parameters    
   would be plotted. You can also set "match=all", in which case all of the    
   parameters are plotted.                                                       
                                                                                 
   Note that the "Sump" command provides a different set of convergence diag-  
   nostics tools that you may also want to explore. Unlike "Plot", "Sump" can
   compare two or more parameter samples and will calculate convergence diagnos- 
   tics as wel as parameter summaries for the pooled sample.                     
                                                                                 
   Options:                                                                      
                                                                                 
   Relburnin     -- If this option is set to 'Yes', then a proportion of the     
                    samples will be discarded as burnin when creating the plot.  
                    The proportion to be discarded is set with Burninfrac (see   
                    Burninfrac below). When the Relburnin option is set to 'No', 
                    then a specific number of samples is discarded instead. This 
                    number is set by Burnin (see below). Note that the burnin    
                    setting is shared across the 'comparetree', 'sump' and 'sumt'
                    commands.                                                    
   Burnin        -- Determines the number of samples (not generations) that will 
                    be discarded when summary statistics are calculated. The     
                    value of this option is only relevant when Relburnin is set  
                    to 'No'.                                                     
   Burninfrac    -- Determines the fraction of samples that will be discarded    
                    when creating a plot. The value of this parameter is only    
                    relevant when Relburnin is set to 'Yes'. Example: A value of 
                    this option of 0.25 means that 25% of the samples will be   
                    discarded.                                                   
   Filename      -- The name of the file to plot.                                
   Parameter     -- Specification of parameters to be plotted. See above for     
                    details.                                                     
   Match         -- Specifies how to match parameter names to the Parameter      
                    specification. See above for details.                        
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter       Options                      Current Setting                  
   ------------------------------------------------------------                  
   Relburnin       Yes/No                       Yes                               
   Burnin          <number>                     0                               
   Burninfrac      <number>                     0.25                           
   Filename        <name>                       temp.p                               
   Parameter       <name>                       lnL                               
   Match           Perfect/Consistentwith/All   Perfect                               
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Prset                                                                         
                                                                                 
   This command sets the priors for the phylogenetic model. Remember that        
   in a Bayesian analysis, you must specify a prior probability distribution     
   for the parameters of the likelihood model. The prior distribution rep-       
   resents your prior beliefs about the parameter before observation of the      
   data. This command allows you to tailor your prior assumptions to a large     
   extent.                                                                       
                                                                                 
   Options:                                                                      
                                                                                 
   Applyto       -- This option allows you to apply the prset commands to        
                    specific partitions. This command should be the first        
                    in the list of commands specified in prset. Moreover, it     
                    only makes sense to be using this command if the data        
                    have been partitioned. A default partition is set on         
                    execution of a matrix. If the data are homogeneous           
                    (i.e., all of the same data type), then this partition       
                    will not subdivide the characters. Up to 30 other part-      
                    itions can be defined, and you can switch among them using   
                    "set partition=<partition name>". Now, you may want to     
                    specify different priors to different partitions of the      
                    data. Applyto allows you to do this. For example, say        
                    you have partitioned the data by codon position, and         
                    you want to fix the statefreqs to equal for the first two    
                    partitions but apply a flat Dirichlet prior to the state-    
                    freqs of the last. This could be implemented in two uses of  
                    prset:                                                       
                                                                                 
                       prset applyto=(1,2) statefreqs=fixed(equal)               
                                                                                 
                       prset applyto=(3) statefreqs=dirichlet(1,1,1,1)           
                                                                                 
                    The first applies the parameters after "applyto"           
                    to the first and second partitions. The second prset         
                    applies a flat Dirichlet to the third partition. You can     
                    also use applyto=(all), which attempts to apply the para-    
                    meter settings to all of the data partitions. Importantly,   
                    if the option is not consistent with the data in the part-   
                    ition, the program will not apply the prset option to        
                    that partition.                                              
   Tratiopr      -- This parameter sets the prior for the transition/trans-      
                    version rate ratio (tratio). The options are:                
                                                                                 
                       prset tratiopr = beta(<number>, <number>)                 
                       prset tratiopr = fixed(<number>)                          
                                                                                 
                    The program assumes that the transition and transversion     
                    rates are independent gamma-distributed random variables     
                    with the same scale parameter when beta is selected. If you  
                    want a diffuse prior that puts equal emphasis on transition/ 
                    transversion rate ratios above 1.0 and below 1.0, then use a 
                    flat Beta, beta(1,1), which is the default. If you wish to   
                    concentrate this distribution more in the equal-rates region,
                    then use a prior of the type beta(x,x), where the magnitude  
                    of x determines how much the prior is concentrated in the    
                    equal rates region. For instance, a beta(20,20) puts more    
                    probability on rate ratios close to 1.0 than a beta(1,1). If 
                    you think it is likely that the transition/transversion rate 
                    ratio is 2.0, you can use a prior of the type beta(2x,x),    
                    where x determines how strongly the prior is concentrated on 
                    tratio values near 2.0. For instance, a beta(2,1) is much    
                    more diffuse than a beta(80,40) but both have the expected   
                    tratio 2.0 in the absence of data. The parameters of the     
                    Beta can be interpreted as counts: if you have observed x    
                    transitions and y transversions, then a beta(x+1,y+1) is a   
                    good representation of this information. The fixed option    
                    allows you to fix the tratio to a particular value.          
   Revmatpr      -- This parameter sets the prior for the substitution rates     
                    of the GTR model for nucleotide data. The options are:       
                                                                                 
                       prset revmatpr = dirichlet(<number>,<number>,...,<number>)
                       prset revmatpr = fixed(<number>,<number>,...,<number>)    
                                                                                 
                    The program assumes that the six substitution rates          
                    are independent gamma-distributed random variables with the  
                    same scale parameter when dirichlet is selected. The six     
                    numbers in brackets each corresponds to a particular substi- 
                    tution type. Together, they determine the shape of the prior.
                    The six rates are in the order A<->C, A<->G, A<->T, C<->G,   
                    C<->T, and G<->T. If you want an uninformative prior you can 
                    use dirichlet(1,1,1,1,1,1), also referred to as a 'flat'     
                    Dirichlet. This is the default setting. If you wish a prior  
                    where the C<->T rate is 5 times and the A<->G rate 2 times   
                    higher, on average, than the transversion rates, which are   
                    all the same, then you should use a prior of the form        
                    dirichlet(x,2x,x,x,5x,x), where x determines how much the    
                    prior is focused on these particular rates. For more info,   
                    see tratiopr. The fixed option allows you to fix the substi- 
                    tution rates to particular values.                           
   Revratepr     -- This parameter sets the prior for each substitution rate of  
                    the GTR model subspace when 'nst' is set to 'mixed' (see the 
                    'lset' command). The only option is                          
                                                                                 
                       prset revratepr = symdir(<number>)                        
                                                                                 
                    which will associate each independent rate in the rate matrix
                    with a modified symmetric Dirichlet prior, where a singleton 
                    rate has the specified alpha parameter, while a rate that    
                    applies to n pairwise substitution types has an alpha that is
                    n times the specified number. The higher the specified num-  
                    ber, the more focused the prior will be on equal rates. The  
                    default value is 1, which gives an effect similar to a flat  
                    Dirichlet.                                                   
   Aamodelpr     -- This parameter sets the rate matrix for amino acid data.     
                    You can either fix the model by specifying aamodelpr=fixed   
                    (<model name>), where <model name> is 'poisson' (a glorified 
                    Jukes-Cantor model), 'jones', 'dayhoff', 'mtrev', 'mtmam',   
                    'wag', 'rtrev', 'cprev', 'vt', 'blosum', 'lg', 'equalin'     
                    (a glorified Felsenstein 1981 model), or 'gtr'. You can also 
                    average over the first ten models by specifying aamodelpr=   
                    mixed. If you do so, the Markov chain will sample each model 
                    according to its probability. The sampled model is reported  
                    as an index: poisson(0), jones(1), dayhoff(2), mtrev(3),     
                    mtmam(4), wag(5), rtrev(6), cprev(7), vt(8), or blosum(9).   
                    The 'Sump' command summarizes the MCMC samples and calculates
                    the posterior probability estimate for each of these models. 
   Aarevmatpr    -- This parameter sets the prior for the substitution rates     
                    of the GTR model for amino acid data. The options are:       
                                                                                 
                       prset aarevmatpr = dirichlet(<number>,<number>,...,<number>)
                       prset aarevmatpr = fixed(<number>,<number>,...,<number>)  
                                                                                 
                    The options are the same as those for 'Revmatpr' except that 
                    they are defined over the 190 rates of the time-reversible   
                    GTR model for amino acids instead of over the 6 rates of the 
                    GTR model for nucleotides. The rates are in the order A<->R, 
                    A<->N, etc to Y<->V. In other words, amino acids are listed  
                    in alphabetic order based on their full name. The first amino
                    acid (Alanine) is then combined in turn with all amino acids 
                    following it in the list, starting with amino acid 2 (Argi-  
                    nine) and finishing with amino acid 20 (Valine). The second  
                    amino acid (Arginine) is then combined in turn with all amino
                    acids following it, starting with amino acid 3 (Asparagine)  
                    and finishing with amino acid 20 (Valine), and so on.        
   Omegapr       -- This parameter specifies the prior on the nonsynonymous/     
                    synonymous rate ratio. The options are:                      
                                                                                 
                       prset omegapr = dirichlet(<number>,<number>)              
                       prset omegapr = fixed(<number>)                           
                                                                                 
                    This parameter is only in effect if the nucleotide sub-      
                    stitution model is set to codon using the lset command       
                    (lset nucmodel=codon). Moreover, it only applies to the      
                    case when there is no variation in omega across sites (i.e., 
                    "lset omegavar=equal").                                    
   Ny98omega1pr  -- This parameter specifies the prior on the nonsynonymous/     
                    synonymous rate ratio for sites under purifying selection.   
                    The options are:                                             
                                                                                 
                       prset Ny98omega1pr = beta(<number>,<number>)              
                       prset Ny98omega1pr = fixed(<number>)                      
                                                                                 
                    This parameter is only in effect if the nucleotide sub-      
                    stitution model is set to codon using the lset command       
                    (lset nucmodel=codon). Moreover, it only applies to the      
                    case where omega varies across sites using the model of      
                    Nielsen and Yang (1998) (i.e., "lset omegavar=ny98"). If   
                    fixing the parameter, you must specify a number between      
                    0 and 1.                                                     
   Ny98omega3pr  -- This parameter specifies the prior on the nonsynonymous/     
                    synonymous rate ratio for positively selected sites. The     
                    options are:                                                 
                                                                                 
                       prset Ny98omega3pr = uniform(<number>,<number>)           
                       prset Ny98omega3pr = exponential(<number>)                
                       prset Ny98omega3pr = fixed(<number>)                      
                                                                                 
                    This parameter is only in effect if the nucleotide sub-      
                    stitution model is set to codon using the lset command       
                    (lset nucmodel=codon). Moreover, it only applies to the      
                    case where omega varies across sites according to the        
                    NY98 model. Note that if the NY98 model is specified         
                    that this parameter must be greater than 1, so you should    
                    not specify a uniform(0,10) prior, for example.              
   M3omegapr     -- This parameter specifies the prior on the nonsynonymous/     
                    synonymous rate ratios for all three classes of sites for    
                    the M3 model. The options are:                               
                                                                                 
                       prset M3omegapr = exponential                             
                       prset M3omegapr = fixed(<number>,<number>,<number>)       
                                                                                 
                    This parameter is only in effect if the nucleotide sub-      
                    stitution model is set to codon using the lset command       
                    (lset nucmodel=codon). Moreover, it only applies to the      
                    case where omega varies across sites using the M3 model of   
                    Yang et al. (2000) (i.e., "lset omegavar=M3"). Under the   
                    exponential prior, the four rates (dN1, dN2, dN3, and dS)    
                    are all considered to be independent draws from the same     
                    exponential distribution (the parameter of the exponential   
                    does not matter, and so you don't need to specify it). The   
                    rates dN1, dN2, and dN3 are taken to be the order statistics 
                    with dN1 < dN2 < dN3. These three rates are all scaled to    
                    the same synonymous rate, dS. The other option is to simply  
                    fix the three rate ratios to some values.                    
   Codoncatfreqs -- This parameter specifies the prior on frequencies of sites   
                    under purifying, neutral, and positive selection. The        
                    options are:                                                 
                                                                                 
                       prset codoncatfreqs = dirichlet(<num>,<num>,<num>)        
                       prset codoncatfreqs = fixed(<number>,<number>,<number>)   
                                                                                 
                    This parameter is only in effect if the nucleotide sub-      
                    stitution model is set to codon using the lset command       
                    (lset nucmodel=codon). Moreover, it only applies to the      
                    case where omega varies across sites using the models of     
                    Nielsen and Yang (1998) (i.e., "lset omegavar=ny98")       
                    or Yang et al. (2000) (i.e., "lset omegavar=M3")           
                    Note that the sum of the three frequencies must be 1.        
   Statefreqpr   -- This parameter specifies the prior on the state freq-        
                    uencies. The options are:                                    
                                                                                 
                       prset statefreqpr = dirichlet(<number>)                   
                       prset statefreqpr = dirichlet(<number>,...,<number>)      
                       prset statefreqpr = fixed(equal)                          
                       prset statefreqpr = fixed(empirical)                      
                       prset statefreqpr = fixed(<number>,...,<number>)          
                                                                                 
                    For the dirichlet, you can specify either a single number    
                    or as many numbers as there are states. If you specify a     
                    single number, then the prior has all states equally         
                    probable with a variance related to the single parameter     
                    passed in.                                                   
   Shapepr       -- This parameter specifies the prior for the gamma/lnorm shape 
                    parameter for among-site rate variation. The options are:    
                                                                                 
                       prset shapepr = uniform(<number>,<number>)                
                       prset shapepr = exponential(<number>)                     
                       prset shapepr = fixed(<number>)                           
                                                                                 
   Pinvarpr      -- This parameter specifies the prior for the proportion of     
                    invariable sites. The options are:                           
                                                                                 
                       prset pinvarpr = uniform(<number>,<number>)               
                       prset pinvarpr = fixed(<number>)                          
                                                                                 
                    Note that the valid range for the parameter is between 0     
                    and 1. Hence, "prset pinvarpr=uniform(0,0.8)" is valid     
                    while "prset pinvarpr=uniform(0,10)" is not. The def-      
                    ault setting is "prset pinvarpr=uniform(0,1)".             
   Ratecorrpr    -- This parameter specifies the prior for the autocorrelation   
                    parameter of the autocorrelated gamma distribution for       
                    among-site rate variation. The options are:                  
                                                                                 
                       prset ratecorrpr = uniform(<number>,<number>)             
                       prset ratecorrpr = fixed(<number>)                        
                                                                                 
                    Note that the valid range for the parameter is between -1    
                    and 1. Hence, "prset ratecorrpr=uniform(-1,1)" is valid    
                    while "prset ratecorrpr=uniform(-11,10)" is not. The       
                    default setting is "prset ratecorrpr=uniform(-1,1)".       
   Covswitchpr   -- This option sets the prior for the covarion switching        
                    rates. The options are:                                      
                                                                                 
                       prset covswitchpr = uniform(<number>,<number>)            
                       prset covswitchpr = exponential(<number>)                 
                       prset covswitchpr = fixed(<number>,<number>)              
                                                                                 
                    The covarion model has two rates: a rate from on to off      
                    and a rate from off to on. The rates are assumed to have     
                    independent priors that individually are either uniformly    
                    or exponentially distributed. The other option is to         
                    fix the switching rates, in which case you must specify      
                    both rates. (The first number is off->on and the second      
                    is on->off).                                                 
   Symdirihyperpr - This option sets the prior for the stationary frequencies    
                    of the states for morphological (standard) data. There can   
                    be as many as 10 states for standard data. However, the      
                    labelling of the states is somewhat arbitrary. For example,  
                    the state "1" for different characters does not have the   
                    same meaning. This is not true for DNA characters, for ex-   
                    ample, where a "G" has the same meaning across characters. 
                    The fact that the labelling of morphological characters is   
                    arbitrary makes it difficult to allow unequal character-     
                    state frequencies. MrBayes gets around this problem by       
                    assuming that the states have a dirichlet prior, with all    
                    states having equal frequency. The variation in the diri-    
                    chlet can be controlled by this parameter--symdirihyperpr.   
                    Symdirihyperpr specifies the distribution on the variance    
                    parameter of the dirichlet. The valid options are:           
                                                                                 
                       prset Symdirihyperpr = uniform(<number>,<number>)         
                       prset Symdirihyperpr = exponential(<number>)              
                       prset Symdirihyperpr = fixed(<number>)                    
                       prset Symdirihyperpr = fixed(infinity)                    
                                                                                 
                    If "fixed(infinity)" is chosen, the dirichlet prior is     
                    fixed such that all character states have equal frequency.   
   Topologypr    -- This parameter specifies the prior probabilities of          
                    phylogenies. The options are:                                
                                                                                 
                       prset topologypr = uniform                                
                       prset topologypr = speciestree                            
                       prset topologypr = constraints(<list>)                    
                       prset topologypr = fixed(<treename>)                      
                                                                                 
                    If the prior is selected to be "uniform", the default,     
                    then all possible trees are considered a priori equally      
                    probable. The 'speciestree' option is used when the topology 
                    is constrained to fold inside a species tree together with   
                    other (gene) trees. The constraints option allows you to     
                    specify complicated prior probabilities on trees (constraints
                    are discussed more fully in "help constraint"). Note that  
                    you must specify a list of constraints that you wish to be   
                    obeyed. The list can be either the constraints' name or      
                    number. Finally, you can fix the topology to that of a user  
                    tree defined in a trees block. Branch lengths will still be  
                    sampled as usual on the fixed topology.                      
   Brlenspr      -- This parameter specifies the prior probability dist-         
                    ribution on branch lengths. The options are specified using: 
                                                                                 
                       prset brlenspr = <setting>                                
                                                                                 
                    where <setting> is one of                                    
                                                                                 
                       unconstrained:uniform(<num>,<num>)                        
                       unconstrained:exponential(<number>)                       
                       unconstrained:twoexp(<num>,<num>)                         
                       unconstrained:gammadir(<num>,<num>,<num>,<num>)           
                       unconstrained:invgamdir(<num>,<num>,<num>,<num>)          
                       clock:uniform                                             
                       clock:birthdeath                                          
                       clock:coalescence                                         
                       clock:fossilization                                       
                       clock:speciestree                                         
                       fixed(<treename>)                                         
                                                                                 
                    Trees with unconstrained branch lengths are unrooted         
                    whereas clock-constrained trees are rooted. The option       
                    after the colon specifies the details of the probability     
                    density of branch lengths. If you choose a birth-death       
                    or coalescence prior, you may want to modify the details     
                    of the parameters of those processes (speciation rate,       
                    extinction rate and sample probability for the birth-death   
                    prior; population size and clock rate parameter for the      
                    coalescence prior). When gene trees are constrained to fold  
                    inside species trees, the appropriate branch length prior is 
                    'clock:speciestree'. Under this model, it is possible to     
                    control whether the population size is constant or variable  
                    across the species tree using the 'popvarpr' setting.        
                    Branch lengths can also be fixed but only if the topology is 
                    fixed.                                                       
                                                                                 
                    For unconstrained branch lengths, MrBayes offers five alter- 
                    native prior distributions. The first two are the simple     
                    'uniform' and 'exponential' priors. The 'uniform' prior takes
                    two parameters, the lower and upper bound of the uniform dis-
                    tribution, respectively. The 'exponential' prior takes a sin-
                    gle parameter, the rate of the exponential distribution. The 
                    mean of the exponential distribution is the inverse of the   
                    rate. For instance, an 'exp(10)' distribution has an expected
                    mean of 0.1.                                                 
                    MrBayes also offers three more complex prior distributions   
                    on unconstrained branch lengths. The two-exponential prior   
                    (Yang and Rannala 2005; Yang 2007) uses two different expo-  
                    nential distributions, one for internal and one for external 
                    branch lengths. The two-exponential prior is invoked using   
                    'twoexp(<r_I>,<r_E>)', where '<r_I>' is a number specifying  
                    the rate of the exponential distribution on internal branch  
                    lengths, while '<r_E>' is the rate for external branch       
                    lengths. The prior mean for internal branch lengths is then  
                    1/r_I, and for external ones is 1/r_E. For instance, to set  
                    prior mean of internal branch lengths to 0.01, and external  
                    ones to 0.1, use 'twoexp(100,10)'.                           
                    The setting 'twoexp(10,10)' is equivalent to 'exp(10)'.      
                    The compound Dirichlet priors 'gammadir(<a_T>,<b_T>,<a>,<c>)'
                    and 'invgamdir(<a_T>,<b_T>,<a>,<c>)' specify a fairly diffuse
                    prior on tree length 'T', and then partition the tree length 
                    into branch lengths according to a Dirichlet distribution    
                    (Rannala et al. 2012). If 'T' is considered drawn from a     
                    gamma distribution with parameters a_T and b_T, and with mean
                    a_T/b_T, we recommend setting a_T = 1; if it is instead con- 
                    sidered drawn from an inverse gamma (invgamma) distribution  
                    with parameters a_T and b_T, and with mean b_T/(a_T -1), then
                    we reccommend setting a_T = 3. In the latter case, b_T should
                    be chosen so that the prior mean of T is reasonable for the  
                    data. In the former case, setting b_T = 0.1 (corresponding to
                    a mean tree length of 10) should be appropriate for a wide   
                    range of tree lengths (at least in the interval 1 to 100).   
                    The concentration parameter a of the Dirichlet distribution  
                    is inversely related to the variance of the branch lengths,  
                    while c is the ratio of the prior means for the internal and 
                    external branch lengths. The default setting, a = c = 1,     
                    specifies a uniform Dirichlet distribution of branch lengths 
                    given the tree length. For instance, 'gammadir(1,0.1,1,1)'   
                    specifies a compound Dirichlet prior on branch lengths, where
                    tree length is associated with a gamma distribution with mean
                    10, and branch length proportions are associated with a uni- 
                    form Dirichlet distribution (default).                       
                                                                                 
                    For clock trees with calibrated external nodes (fossils),    
                    MrBayes also offers the fossilized birth-death prior:        
                    'clock:fossilization'.                                       
                    If 'SampleStrat' is set to 'fossiltip', it assumes that upon 
                    sampling the lineage is dead and won't produce descendants,  
                    meaning each fossil sample is a tip. If 'SampleStrat' is set 
                    to 'random' (default), fossils are sampled serially along the
                    birth-death tree (Stadler 2010), so they can be tips or an-  
                    cestors. See 'Speciationpr', 'Extinctionpr', 'SampleStrat',  
                    'Fossilizationpr' for more information.                      
                                                                                 
   Treeagepr     -- This parameter specifies the prior probability distribution  
                    on the tree age when a uniform or fossilization prior is used
                    on the branch lengths of a clock tree.                       
                                                                                 
                    The options are:                                             
                                                                                 
                       prset treeagepr = <setting>                               
                                                                                 
                    where <setting> is one of                                    
                                                                                 
                       fixed(<age>)                                              
                       uniform(<min_age>,<max_age>)                              
                       offsetexponential(<min_age>,<mean_age>)                   
                       truncatednormal(<min_age>,<mean_age>,<st.dev.>)           
                       lognormal(<mean_age>,<st.dev.>)                           
                       offsetlognormal(<min_age>,<mean_age>,<st.dev.>)           
                       gamma(<mean_age>,<st.dev.>)                               
                       offsetgamma(<min_age>,<mean_age>,<st.dev.>)               
                                                                                 
                    These are the same options used for the 'Calibrate' command. 
                    Note that, unlike elsewhere in MrMayes, we always use the    
                    mean and standard deviation of the resulting age distribution
                    rather than the standard parameterization, if different. This
                    is to facilitate for the users who want to focus on the in-  
                    formation conveyed about the age. For those who wish to use  
                    the standard parameterization, there are simple conversions  
                    between the two. See the 'Calibrate' command for more infor- 
                    mation.                                                      
                                                                                 
                    The tree age is simply the age of the most recent common     
                    ancestor of the tree. If the clock rate is fixed to 1.0,     
                    which is the default, the tree age is equivalent to the      
                    expected number of substitutions from the root to the tip of 
                    the tree, that is, tree height. The tree age prior ensures   
                    that the joint probability for the uniform prior (or fossil- 
                    ization prior) model of branch lengths on a clock tree is    
                    proper. The default setting is 'gamma(1,1)'. If the root node
                    in the tree is calibrated, the root calibration replaces the 
                    tree age prior.                                              
   Speciationpr  -- This parameter sets the prior on the net speciation rate (net
                    diversification), that is, (lambda - mu) in the birth-death  
                    model and the general case of fossilized birth-death model.  
                    Or, (lambda - mu - psi) in the special case of f-b-d model   
                    (fossiltip). Values of this parameter are > 0. Prior options:
                                                                                 
                       prset speciationpr = uniform(<number>,<number>)           
                       prset speciationpr = exponential(<number>)                
                       prset speciationpr = fixed(<number>)                      
                                                                                 
                    This parameter is only relevant if the (fossil) birth-death  
                    process is selected as the prior on branch lengths.          
   Extinctionpr  -- This parameter sets the prior on the relative extinction rate
                    (turnover), that is, (mu / lambda) in the birth-death model  
                    and the general case of fossilized birth-death model.        
                    Or, (mu + psi) / lambda in the special case of f-b-d model   
                    (fossiltip). Values of this parameter are in range (0,1).    
                                                                                 
                       prset extinctionpr = beta(<number>,<number>)              
                       prset extinctionpr = fixed(<number>)                      
                                                                                 
                    This parameter is only relevant if the (fossil) birth-death  
                    process is selected as the prior on branch lengths.          
 Fossilizationpr -- This parameter sets the prior on the relative fossilization  
                    rate (sampling proportion), psi/(mu+psi), in the fossilized  
                    b-d model. Values of this parameter are in range (0,1).      
                    If SampleStrat is used to divide up time intervals, it sets  
                    the prior for the fossilization parameter in each interval.  
                                                                                 
                       prset fossilizationpr = beta(<number>,<number>)           
                       prset fossilizationpr = fixed(<number>)                   
                                                                                 
                    This parameter is only relevant if the fossilized birth-death
                    process is selected as the prior on branch lengths.          
   SampleStrat   -- This parameter sets the strategy under which species were    
                    sampled in the analysis. For the birth-death prior, 'birth-  
                    death' (Hohna et al. 2011), three strategies: 'random',      
                    'diversity' and 'cluster' sampling can be used for extant    
                    taxa. No extinct sample (fossil) is allowed in this prior.   
                    For data with extant and extinct samples, use 'prset brlenspr
                    =clock:fossilization'. (Stadler 2010; Zhang et al. 2015)     
                    For the fossilized birth-death prior, 'fossiltip' assumes    
                    extant taxa are sampled randomly, and extinct taxa (fossils) 
                    are sampled with constant rate and upon sampling the lineage 
                    is dead and won't produce any descendant. So fossils are all 
                    at tips. Except 'fossiltip', the following strategies allow  
                    fossils also being ancestors of other samples.               
                    'random' (default) assumes extant taxa are sampled randomly  
                    with prob rho, while fossils are sampled on the birth-death  
                    tree with piecewise constant rates, psi_i (i = 1,...,s+1).   
                    'diversity' assumes extant taxa are sampled to maximize      
                    diversity, while fossils are sampled randomly.               
                    Time is divided by <s> slice samping events in the past, each
                    at time <t_i> with probability <rho_i> (s >= 0). If rho_i = 0
                    the slice is only used to divide up time intervals not for   
                    sampling of fossils.  Extant taxa are sampled with prob.     
                    (proportion) rho (set in sampleprob).                        
                                                                                 
                       prset samplestrat = random                                
                       prset samplestrat = diversity                             
                       prset samplestrat = cluster                               
                       prset samplestrat = fossiltip                             
                       prset samplestrat = random    <s>:...,<t_i> <rho_i>,...   
                       prset samplestrat = diversity <s>:...,<t_i> <rho_i>,...   
                                                                                 
   Sampleprob    -- This parameter sets the fraction of extant species that are  
                    sampled in the analysis. This is used with the birth-death   
                    prior on trees (Yang and Rannala 1997; Stadler 2009; Hohna   
                    et al. 2011), and the fossilized birth-death prior (Stadler  
                    2010, Zhang et al. 2015).                                    
                                                                                 
                       prset sampleprob = <number>                               
                                                                                 
   Popsizepr     -- This parameter sets the prior on the population size compo-  
                    nent of the coalescent parameter. The options are:           
                                                                                 
                       prset popsizepr = uniform(<number>,<number>)              
                       prset popsizepr = lognormal(<number>,<number>)            
                       prset popsizepr = normal(<number>,<number>)               
                       prset popsizepr = gamma(<number>,<number>)                
                       prset popsizepr = fixed(<number>)                         
                                                                                 
                    This parameter is only relevant if the coalescence process is
                    selected as the prior on branch lengths. Note that the set-  
                    ting of 'ploidy' in 'lset' is important for how this para-   
                    meter is interpreted.                                        
   Popvarpr      -- In a gene tree - species tree model, this parameter deter-   
                    mines whether the population size is the same for the entire 
                    species tree ('popvarpr = equal', the default), or varies    
                    across branches of the species tree ('popvarpr=variable').   
   Nodeagepr     -- This parameter specifies the assumptions concerning the age  
                    of the terminal and interior nodes in the tree. The default  
                    model ('nodeagepr = unconstrained') assumes that all terminal
                    nodes are of the same age while the age of interior nodes is 
                    unconstrained. The alternative ('nodeagepr = calibrated')    
                    option derives a prior probability distribution on terminal  
                    and interior node ages from the calibration settings (see    
                    the 'calibrate' command). The 'nodeagepr' parameter is only  
                    relevant for clock trees.                                    
   Clockratepr   -- This parameter specifies the prior assumptions concerning the
                    base substitution rate of the tree, measured in expected num-
                    ber of substitutions per site per time unit. The default set-
                    ting is 'Fixed(1.0)', which effectively means that the time  
                    unit is the number of expected substitutions per site.       
                    If you do not have any age calibrations in the tree, you can 
                    still calibrate the tree using 'Clockratepr'. For instance,  
                    if you know that your sequence data evolve at a rate of 0.20 
                    substitutions per million years, you might calibrate the tree
                    by fixing the substitution rate to 0.20 using                
                                                                                 
                       prset clockratepr = fixed(0.20)                           
                                                                                 
                    after which the tree will be calibrated using millions of    
                    years as the unit.                                           
                                                                                 
                    You can also assign a prior probability distribution to the  
                    substitution rate, accommodating the uncertainty of it.      
                    When you calibrate the nodes, you should properly set this   
                    prior to match the time unit of the calibrations.            
                    You can choose among normal, lognormal, exponential and gamma
                    distributions for this purpose. For instance, to assign a    
                    normal distribution truncated at 0, so that only positive    
                    values are allowed, and with mean 0.20 and standard deviation
                    of 0.02, you would use                                       
                                                                                 
                       prset clockratepr = normal(0.20,0.02)                     
                                                                                 
                    The lognormal distribution is parameterized in terms of the  
                    mean and standard deviation on the log scale (natural logs). 
                    For instance,                                                
                                                                                 
                       prset clockratepr = lognormal(-1.61,0.10)                 
                                                                                 
                    specifies a lognormal distribution with a mean of log values 
                    of -1.61 and a standard deviation of log values of 0.10. In  
                    such a case, the mean value of the lognormal distribution is 
                    equal to e^(-1.61 + 0.10^2/2) = 0.20.                        
                                                                                 
                    Note that the 'Clockratepr' parameter has no effect on non-  
                    clock trees.                                                 
   Clockvarpr    -- This parameter allows you to specify the type of clock you   
                    are assuming. The default is 'strict', which corresponds to  
                    the standard clock model where the evolutionary rate is      
                    constant throughout the tree. For relaxed clock models, you  
                    can use 'cpp', 'tk02', 'igr'. ('mixed' is not working)       
                    'cpp' invokes a relaxed clock model where the rate evolves   
                    according to a Compound Poisson Process (CPP) (Huelsenbeck   
                    et al., 2000).                                               
                    'tk02' invokes the Brownian Motion model described by Thorne 
                    and Kishino (2002). [autocorrelated lognormal distributions] 
                    'igr' invokes the Independent Gamma Rate (IGR) model where   
                    each branch has an independent rate drawn from a gamma       
                    distribution (LePage et al., 2007).                          
                    Each of the relaxed clock models has additional parameters   
                    with priors. For the CPP model, it is 'cppratepr' and        
                    'cppmultdevpr'; for the TK02 model, it is 'tk02varpr'; for   
                    the IGR  model, it is 'igrvarpr'.                            
                    The 'clockvarpr' parameter is only relevant for clock trees. 
                                                                                 
                    For backward compatibility, 'bm' is allowed as a synonym of  
                    'tk02', and 'ibr' as a synonym of 'igr'.                     
   Cppratepr     -- This parameter allows you to specify a prior probability     
                    distribution on the rate of the Poisson process generating   
                    changes in the evolutionary rate in the CPP relaxed clock    
                    model. You can either fix the rate or associate it with an   
                    exponential prior using                                      
                                                                                 
                       prset cppratepr = fixed(<number>)                         
                       prset cppratepr = exponential(<number>)                   
                                                                                 
                    For instance, if you fix the rate to 2, then on a branch     
                    with the length equual to one expresed in terms of average   
                    expected number of substitution per site, you expect to see, 
                    on average, two rate-modifying events.                       
                    If you put an exponential(0.1) on the rate, you will be      
                    estimating the rate against a prior probability distribution 
                    where the expected rate is 10 (= 1/0.1).                     
   Cppmultdevpr  -- This parameter allows you to specify the standard deviation  
                    of the log-normal distribution from which the rate multi-    
                    pliers of the CPP relaxed clock model are drawn. The standard
                    deviation is given on the log scale. The default value of 1.0
                    thus corresponds to rate multipliers varying from 0.37 (1/e) 
                    to 2.7 (e) when they are +/- one standard deviation from the 
                    expected mean. The expected mean of the logarithm of the mul-
                    pliers is fixed to 0, ensuring that the expected mean rate is
                    1.0. You can change the default value by using               
                                                                                 
                       prset cppmultdevpr = fixed(<number>)                      
                                                                                 
                    where <number> is the standard deviation on the log scale.   
   TK02varpr     -- This parameter allows you to specify the prior probability   
                    distribution for the variance of the rate multiplier in the  
                    Thorne-Kishino ('Brownian motion') relaxed clock model.      
                    Specifically, the parameter specifies the rate at which the  
                    variance increases with respect to the base rate of the      
                    clock. If you have a branch of a length corresponding to 0.4 
                    expected changes per site according to the base rate of the  
                    clock, and the tk02var parameter has a value of 2.0, then the
                    rate multiplier at the end of the branch will be drawn from a
                    lognormal distribution with a variance of 0.4*2.0 (on the    
                    linear, not the logarithm scale). The mean is the same as the
                    rate multiplier at the start of the branch (again on the     
                    linear scale).                                               
                                                                                 
                    You can set the parameter to a fixed value, or specify that  
                    it is drawn from an exponential or uniform distribution:     
                                                                                 
                       prset tk02varpr = fixed(<number>)                         
                       prset tk02varpr = exponential(<number>)                   
                       prset tk02varpr = uniform(<number>,<number>)              
                                                                                 
                    For backward compatibility, 'bmvarpr' is allowed as a synonym
                    of 'tko2varpr'.                                              
   Igrvarpr      -- This parameter allows you to specify a prior on the variance 
                    of the gamma distribution from which the branch lengths are  
                    drawn in the independent branch rate (IGR) relaxed clock     
                    model. Specifically, the parameter specifies the rate at     
                    which the variance increases with respect to the base rate of
                    the clock. If you have a branch of a length corresponding to 
                    0.4 expected changes per site according to the base rate of  
                    the clock, and the igrvar parameter has a value of 2.0, then 
                    the effective branch length will be drawn from a distribution
                    with a variance of 0.4*2.0.                                  
                                                                                 
                    You can set the parameter to a fixed value, or specify that  
                    it is drawn from an exponential or uniform distribution:     
                                                                                 
                       prset igrvarpr = fixed(<number>)                          
                       prset igrvarpr = exponential(<number>)                    
                       prset igrvarpr = uniform(<number>,<number>)               
                                                                                 
                    For backward compatibility, 'ibrvarpr' is allowed as a syn-  
                    onym of 'igrvarpr'.                                          
   Ratepr        -- This parameter allows you to specify the site specific rates 
                    model or any other model that allows different partitions to 
                    evolve at different rates. First, you must have defined a    
                    partition of the characters. For example, you may define a   
                    partition that divides the characters by codon position, if  
                    you have DNA data. You can also divide your data using a     
                    partition that separates different genes from each other.    
                    The next step is to make the desired partition the active one
                    using the set command. For example, if your partition is     
                    called "by_codon", then you make that the active partition 
                    using "set partition=by_codon". Now that you have defined  
                    and activated a partition, you can specify the rate multi-   
                    pliers for the various partitions. The options are:          
                                                                                 
                       prset ratepr = fixed                                      
                       prset ratepr = variable                                   
                       prset ratepr = dirichlet(<number>,<number>,...,<number>)  
                                                                                 
                    If you specify "fixed", then the rate multiplier for       
                    that partition is set to 1 (i.e., the rate is fixed to       
                    the average rate across partitions). On the other hand,      
                    if you specify "variable", then the rate is allowed to     
                    vary across partitions subject to the constraint that the    
                    average rate of substitution across the partitions is 1.     
                    You must specify a variable rate prior for at least two      
                    partitions, otherwise the option is not activated when       
                    calculating likelihoods. The variable option automatically   
                    associates the partition rates with a dirichlet(1,...,1)     
                    prior. The dirichlet option is an alternative way of setting 
                    a partition rate to be variable, and also gives accurate     
                    control of the shape of the prior. The parameters of the     
                    Dirichlet are listed in the order of the partitions that the 
                    ratepr is applied to. For instance, "prset applyto=(1,3,4)  
                    ratepr = dirichlet(10,40,15)" would set the Dirichlet para- 
                    meter 10 to partition 1, 40 to partition 3, and 15 to parti- 
                    tion 4. The Dirichlet distribution is applied to the weighted
                    rates; that is, it weights the partition rates according to  
                    the number of included characters in each partition.         
   Generatepr    -- This parameter is similar to 'Ratepr' but applies to gene    
                    trees in the multispecies coalescent, whereas 'Ratepr' app-  
                    lies to partitions within genes.                             
                                                                                 
   Default model settings:                                                       
                                                                                 
   Parameter        Options                      Current Setting                 
   ------------------------------------------------------------------            
   Tratiopr         Beta/Fixed                   Beta(1.0,1.0)
   Revmatpr         Dirichlet/Fixed              Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0)
   Aamodelpr        Fixed/Mixed                  Fixed(Poisson)
   Aarevmatpr       Dirichlet/Fixed              Dirichlet(1.0,1.0,...)
   Omegapr          Dirichlet/Fixed              Dirichlet(1.0,1.0)
   Ny98omega1pr     Beta/Fixed                   Beta(1.0,1.0)
   Ny98omega3pr     Uniform/Exponential/Fixed    Exponential(1.0)
   M3omegapr        Exponential/Fixed            Exponential
   Codoncatfreqs    Dirichlet/Fixed              Dirichlet(1.0,1.0,1.0)
   Statefreqpr      Dirichlet/Fixed              Dirichlet(1.0,1.0,1.0,1.0)
   Shapepr          Uniform/Exponential/Fixed    Exponential(1.0)
   Ratecorrpr       Uniform/Fixed                Uniform(-1.0,1.0)
   Pinvarpr         Uniform/Fixed                Uniform(0.0,1.0)
   Covswitchpr      Uniform/Exponential/Fixed    Uniform(0.0,100.0)
   Symdirihyperpr   Uniform/Exponential/Fixed    Fixed(Infinity)
   Topologypr       Uniform/Constraints/Fixed/   Uniform
                    Speciestree                  
   Brlenspr         Unconstrained/Clock/Fixed    Unconstrained:GammaDir(1.0,0.100,1.0,1.0)
   Treeagepr        Gamma/Uniform/Fixed/         Gamma(1.00,1.00)
                    Truncatednormal/Lognormal/   
                    Offsetlognormal/Offsetgamma/ 
                    Offsetexponential            
   Speciationpr     Uniform/Exponential/Fixed    Exponential(1.0)
   Extinctionpr     Beta/Fixed                   Beta(1.0,1.0)
   Fossilizationpr  Beta/Fixed                   Beta(1.0,1.0)
   SampleStrat      Random/Diversity/Cluster/    Random
                    FossilTip                    
   Sampleprob       <number>                     1.00000000
   Popsizepr        Lognormal/Gamma/Uniform/     Gamma(1.0,10.0)
                    Normal/Fixed                 
   Popvarpr         Equal/Variable               Equal
   Nodeagepr        Unconstrained/Calibrated     Unconstrained
   Clockratepr      Fixed/Normal/Lognormal/      Fixed(1.00)
                    Exponential/Gamma            
   Clockvarpr       Strict/Cpp/TK02/Igr/Mixed    Strict
   Cppratepr        Fixed/Exponential            Exponential(0.10)
   Cppmultdevpr     Fixed                        Fixed(0.40)
   TK02varpr        Fixed/Exponential/Uniform    Exponential(1.00)
   Igrvarpr         Fixed/Exponential/Uniform    Exponential(10.00)
   Ratepr           Fixed/Variable=Dirichlet     Fixed
   Generatepr       Fixed/Variable=Dirichlet     Fixed
   ------------------------------------------------------------------            
                                                                                 
   ---------------------------------------------------------------------------   
   Propset                                                                       
                                                                                 
   This command allows the user to change the details of the MCMC samplers       
   (moves) that update the state of the chain. The useage is:                    
                                                                                 
      propset  <move_name>$<tuning-parameter>=<value>                            
                                                                                 
   Assume we have a topology parameter called 'Tau{all}', which is sampled by    
   the move 'ExtTBR(Tau{all})' (note that the parameter name is included in the  
   move name). This move has three tuning parameters: (1) 'prob', the relative   
   proposal probability (a weight defining its probability relative to other     
   moves); (2) 'p_ext', the extension probability; and (3) 'lambda', the tuning  
   parameter of the branch length multiplier. A list of the tuning parameters is 
   available by using 'Showmoves' (see below). To change the relative proposal   
   probability to 20 and the extension probability to 0.7, use:                  
                                                                                 
      propset etbr(tau{all})$prob=20 etbr(tau{all})$p_ext=0.7                    
                                                                                 
   This change would apply to all chains in all runs. It is also possible to set 
   the tuning parameters of individual runs and chains using the format:         
                                                                                 
      propset  <move_name>$<tuning-parameter>(<run>,<chain>)=<value>             
                                                                                 
   where <run> and <chain> are the index numbers of the run and chain for which  
   you want to change the value. If you leave out the index of the run, the      
   change will apply to all runs; if you leave out the index of the chain, the   
   change will similarly apply to all chains. To switch off the exttbr(tau{all}) 
   move in chain 2 of all runs, use:                                             
                                                                                 
      propset  etbr(tau{all})$prob(,2)=0                                         
                                                                                 
   It is important to note that all moves are not available until the model has  
   been completely defined. Any change to the model will cause all proposal      
   tuning parameters to return to their default values. To see a list of all the 
   moves that are currently switched on for the model, use 'showmoves'. You can  
   also see other available moves by using 'showmoves allavailable=yes'. A list  
   of the moves for each parameter in the model is available by using the command
   'Showparams'. If you change proposal probabilities, make sure that all        
   parameters that are not fixed in your model have at least one move switched   
   on.                                                                           
                                                                                 
   One word of warning: You should be extremely careful when modifying any       
   of the chain parameters using 'propset'. It is quite possible to completely   
   wreck any hope of achieving convergence by inappropriately setting the        
   tuning parameters. In general, you want to set move tuning parameters such    
   that the acceptance rate of the move is intermediate (we suggest targeting    
   the range 10% to 70% acceptance, if possible). If the acceptance rate is    
   outside of this range, the MCMC chain will probably not sample that parameter 
   very efficiently. The acceptance rates for all moves in the cold chain(s) are 
   summarized at the end of each run in the screen output. The acceptance rates  
   (potentially for all chains, cold and heated) are also printed to the .mcmc   
   file if Mcmc convergence diagnostics are turned on (using 'Mcmc' or 'Mcmcp'). 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Quit                                                                          
                                                                                 
   This command quits the program. The correct usage is:                         
                                                                                 
      quit                                                                       
                                                                                 
   It is a very easy command to use properly.                                    
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Report                                                                        
                                                                                 
   This command allows you to control how the posterior distribution is          
   reported. For rate parameters, it allows you to choose among several popular  
   parameterizations. The report command also allows you to request printing of  
   some model aspects that are usually not reported. For instance, if a node is  
   constrained in the analysis, MrBayes can print the probabilities of the       
   ancestral states at that node. Similarly, if there is rate variation in the   
   model, MrBayes can print the inferred site rates, and if there is omega varia-
   tion, MrBayes can print the inferred omega (positive selection) values for    
   each codon. In a complex model with several partitions, each partition is     
   controlled separately using the same 'Applyto' mechanism as in the 'Lset' and 
   'Prset' commands.                                                             
                                                                                 
   Options:                                                                      
                                                                                 
   Applyto   -- This option allows you to apply the report commands to specific  
                partitions. This command should be the first in the list of      
                commands specified in 'report'.                                  
                For example,                                                     
                                                                                 
                   report applyto=(1,2) tratio=ratio                             
                                                                                 
                   report applyto=(3) tratio=dirichlet                           
                                                                                 
                would result in the transition and transversion rates of the     
                first and second partitions in the model being reported as a     
                ratio and the transition and transversion rates of the third     
                partition being reported as proportions of the rate sum (the     
                Dirichlet parameterization).                                     
   Tratio    -- This specifies the report format for the transition and trans-   
                version rates of a nucleotide substituion model with nst=2.      
                If 'ratio' is selected, the rates will be reported as a ratio    
                (transition rate/transversion rate). If 'dirichlet' is selected, 
                the transition and transversion rates will instead be reported   
                as proportions of the rate sum. For example, if the transition   
                rate is three times the transversion rate and 'ratio' is selec-  
                ted, this will reported as a single value, '3.0'. If 'dirichlet' 
                is selected instead, the same rates will be reported using two   
                values, '0.75 0.25'. The sum of the Dirichlet values is always 1.
                Although the Dirichlet format may be unfamiliar to some users,   
                it is more convenient for specifying priors than the ratio       
                format.                                                          
   Revmat    -- This specifies the report format for the substitution rates of   
                a GTR substitution model for nucleotide or amino acid data. If   
                'ratio' is selected, the rates will be reported scaled to the    
                G-T rate (for nucleotides) or the Y-V rate (for amino acids). If 
                'dirichlet' is specified instead, the rates are reported as pro- 
                portions of the rate sum. For instance, assume that the C-T rate 
                is twice the A-G rate and four times the transversion rates,     
                which are equal. If the report format is set to 'ratio', this    
                would be reported as '1.0 2.0 1.0 1.0 4.0 1.0' since the rates   
                are reported in the order rAC, rAG, rAT, rCG, rCT, rGT and scaled
                relative to the last rate, the G-T rate. If 'dirichlet' is selec-
                ted instead, the same rates would have been reported as '0.1 0.2 
                0.1 0.1 0.4 0.1' since the rates are now scaled so that they sum 
                to 1.0. The Dirichlet format is the parameterization used for    
                formulating priors on the rates.                                 
   Ratemult  -- This specifies the report format used for the rate multiplier of 
                different model partitions. Three formats are available. If      
                'scaled' is selected, then rates are scaled such that the mean   
                rate per site across partitions is 1.0. If 'ratio' is chosen,    
                the rates are scaled relative to the rate of the first parti-    
                tion. Finally, if 'dirichlet' is chosen, the rates are given as  
                proportions of the rate sum. The latter is the format used       
                when formulating priors on the rate multiplier.                  
   Tree      -- This specifies the report format used for the tree(s). Two op-   
                tions are available. 'Topology' results in only the topology     
                being printed to file, whereas 'brlens' causes branch lengths to 
                to be printed as well.                                           
   Ancstates -- If this option is set to 'yes', MrBayes will print the pro-      
                bability of the ancestral states at all constrained nodes. Typ-  
                ically, you are interested in the ancestral states of only a few 
                characters and only at one node in the tree. To perform such     
                an analysis, first define and enforce a topology constraint      
                using 'constraint' and 'prset topologypr = constraints (...)'.   
                Then put the character(s) of interest in a separate partition and
                set MrBayes to report the ancestral states for that partition.   
                For instance, if the characters of interest are in partition 2,  
                use 'report applyto=(2) ancstates=yes' to force MrBayes to print 
                the probability of the ancestral states of those characters at   
                the constrained node to the '.p' file.                           
   Siterates -- If this option is set to 'yes' and the relevant model has rate   
                variation across sites, then the site rates, weighted over rate  
                categories, will be reported to the '.p' file.                   
   Possel    -- If this option is set to 'yes' and the relevant model has omega  
                variation across sites, the probability that each model site     
                (codon in this case) is positively selected will be written to   
                file.                                                            
   Siteomega -- If this option is set to 'yes' and the relevant model has omega  
                variation across sites, the weighted omega value (over omega     
                categories) for each model site will be reported to file.        
                                                                                 
   Default report settings:                                                       
                                                                                 
   Parameter       Options                  Current Setting                      
   --------------------------------------------------------                      
   Tratio          Ratio/Dirichlet          Ratio                                   
   Revmat          Ratio/Dirichlet          Dirichlet                                   
   Ratemult        Scaled/Ratio/Dirichlet   Scaled                                   
   Tree            Brlens/Topology          Brlens                                   
   Ancstates       Yes/No                   No                                   
   Siterates       Yes/No                   No                                   
   Possel          Yes/No                   No                                   
   Siteomega       Yes/No                   No                                   
                                                                                 
   ------------------------------------------------------------------            
   ---------------------------------------------------------------------------   
   Restore                                                                       
                                                                                 
   This command restores taxa to the analysis. The correct usage is:             
                                                                                 
      restore <name and/or number and/or taxset> ...                             
                                                                                 
   A list of the taxon names or taxon numbers (labelled 1 to ntax in the order   
   in the matrix) or taxset(s) can be used.  For example, the following:         
                                                                                 
      restore 1 2 Homo_sapiens                                                   
                                                                                 
   restores taxa 1, 2, and the taxon labelled Homo_sapiens to the analysis.      
   You can also use "all" to restore all of the taxa. For example,             
                                                                                 
      restore all                                                                
                                                                                 
   restores all of the taxa to the analysis.                                     
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Set                                                                           
                                                                                 
   This command is used to set some general features of the model or program     
   behavior. The correct usage is                                                
                                                                                 
      set <parameter>=<value> ... <parameter>=<value>                            
                                                                                 
   Available options:                                                            
                                                                                 
   Seed         -- Sets the seed number for the random number generator. The     
                   random number seed is initialized haphazardly at the beg-     
                   inning of each MrBayes session. This option allows you to     
                   set the seed to some specific value, thereby allowing you     
                   to exactly repeat an analysis. If the analysis uses swapping  
                   between cold and heated chains, you must also set the swap    
                   seed (see below) to exactly repeat the analysis.              
   Swapseed     -- Sets the seed used for generating the swapping sequence       
                   when Metropolis-coupled heated chains are used. This seed     
                   is initialized haphazardly at the beginning of each MrBayes   
                   session. This option allows you to set the seed to some       
                   specific value, thereby allowing you to exactly repeat a      
                   swap sequence. See also the 'Seed' option.                    
   Dir          -- The working directory. Specifies the absolute or relative path
                   to the working directory. If left empty, the working directory
                   is the current directory.                                     
   Partition    -- Set this option to a valid partition id, either the number or 
                   name of a defined partition, to enforce a specific partition- 
                   ing of the data. When a data matrix is read in, a partition   
                   called "Default" is automatically created. It divides the   
                   data into one part for each data type. If you only have one   
                   data type, DNA for instance, the default partition will not   
                   divide up the data at all. The default partition is always    
                   the first partition, so 'set partition=1' is the same as      
                   'set partition=default'.                                      
   Speciespartition -- Set this option to a valid speciespartition id, either the
                   number or name of a defined speciespartition, to enforce a    
                   specific partitioning of taxa to species. When a data matrix  
                   is read in, a speciespartition called "Default" is auto-    
                   matically created. It assigns one taxon for each species. The 
                   default speciespartition is always the first speciespartition,
                   so 'set speciespartition=1' is the same as                    
                   'set speciespartition=default'.                               
   Autoclose    -- If autoclose is set to 'yes', then the program will not prompt
                   you during the course of executing a file. This is particular-
                   ly useful when you run MrBayes in batch mode.                 
   Nowarnings   -- If nowarnings is set to yes, then the program will not prompt 
                   you when overwriting or appending an ouput file that is al-   
                   ready present. If 'nowarnings=no' (the default setting), then 
                   the program propts the user before overwriting output files.  
   Autoreplace  -- When nowarnings is set to yes, then MrBayes will by default   
                   overwrite output files that already exists. This may cause    
                   irrecoverable loss of previous results if you have not removed
                   or renamed the files from previous runs. To override this be- 
                   havior, set autoreplace to no, in which case new output will  
                   be appended to existing files instead.                        
   Quitonerror  -- If quitonerror is set to yes, then the program will quit when 
                   an error is encountered, after printing an error message. If  
                   quitonerror is set to no (the default setting), then the      
                   program will wait for additional commands from the command    
                   line after the error message is printed.                      
   Scientific   -- Set this option to 'Yes' to write sampled values to file in   
                   scientific format and to 'No' to write them in fixed format.  
                   Fixed format is easier for humans to read but you risk losing 
                   precision for small numbers. For instance, sampled values that
                   are less than 1E-6 will print to file as '0.000000' if fixed  
                   format is used and 'precision' is set to 6.                   
   Precision    -- Precision allows you to set the number of decimals to be prin-
                   ted when sampled values are written to file. Precision must be
                   in the range 3 to 15.                                         
   Usebeagle    -- Set this option to 'Yes' to attempt to use the BEAGLE library 
                   to compute the phylogenetic likelihood on a variety of high-  
                   performance hardware including multicore CPUs and GPUs. Some  
                   models in MrBayes are not yet supported by BEAGLE.            
   Beagleresource -- Set this option to the number of a specific resource you    
                   wish to use with BEAGLE (use 'Showbeagle' to see the list of  
                   available resources). Set to '99' for auto-resource selection.
   Beagledevice -- Set this option to 'GPU' or 'CPU' to select processor.        
   Beagleprecision -- Selection 'Single' or 'Double' precision computation.      
   Beaglescaling -- 'Always' rescales partial likelihoods at each evaluation.    
                    'Dynamic' rescales less frequently and should run faster.    
   Beaglesse    -- Use SSE instructions on Intel CPU processors.                 
   Beagleopenmp -- Use OpenMP to parallelize across multi-core CPU processors.   
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter          Options               Current Setting                      
   --------------------------------------------------------                      
   Seed               <number>              1428420230                                  
   Swapseed           <number>              1428420230                                  
   Dir                <name>                ""
   Partition          <name>                ""
   Speciespartition   <name>                ""
   Autoclose          Yes/No                No                                   
   Nowarnings         Yes/No                No                                   
   Autoreplace        Yes/No                Yes                                   
   Quitonerror        Yes/No                No                                   
   Scientific         Yes/No                Yes                                   
   Precision          <number>              6                                   
   Usebeagle          Yes/No                No                                   
   Beagleresource     <number>              99                                   
   Beagledevice       CPU/GPU               CPU                                   
   Beagleprecision    Single/Double         Double                                   
   Beaglescaling      Always/Dynamic        Always                                   
   Beaglesse          Yes/No                No                                   
   Beagleopenmp       Yes/No                No                                   
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Showbeagle                                                                    
                                                                                 
   This command shows available BEAGLE resources.                                
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Showmatrix                                                                    
                                                                                 
   This command shows the character matrix currently in memory.                  
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Showmcmctrees                                                                 
                                                                                 
   This command shows the current trees used by the Markov chains.               
   is "showmcmctrees".                                                         
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Showmodel                                                                     
                                                                                 
   This command shows the current model settings. The correct usage is           
                                                                                 
      showmodel                                                                  
                                                                                 
   After typing "showmodel", the modelling assumptions are shown on a          
   partition-by-partition basis.                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Showmoves                                                                     
                                                                                 
   This command shows the MCMC samplers (moves) that are switched on for the     
   parameters in the current model. The basic usage is                           
                                                                                 
      showmoves                                                                  
                                                                                 
   If you want to see all available moves, use                                   
                                                                                 
      showmoves allavailable=yes                                                 
                                                                                 
   If you want to change any of the tuning parameters for the moves, use the     
   'propset' command.                                                            
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Showparams                                                                    
                                                                                 
   This command shows all of the parameters in the current model. The basic      
   usage is                                                                      
                                                                                 
      showparams                                                                 
                                                                                 
   The parameters are listed together with their priors, the available moves,    
   and the current value(s), which will be used as the starting values in the    
   next mcmc analysis.                                                           
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Showusertrees                                                                 
                                                                                 
   This command shows the currently defined user trees. The correct usage        
   is "showusertrees".                                                         
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Speciespartition                                                              
                                                                                 
   Defines a partition of tips into species. The format for the speciespartition 
   command is                                                                    
                                                                                 
      Speciespartition <name> = <species name>:<taxon list> ,...,<sp nm>:<tx lst>
                                                                                 
   The command enumerates comma separated list of pairs consisting of 'species   
   name' and 'taxon list'. The 'taxon list' is a standard taxon list, as used by 
   the 'Taxset' command. This means that you can use either the index or the name
   of a sequence ('taxon'). Ranges are specified using a dash, and a period can  
   be used as a synonym of the last sequence in the matrix.                      
                                                                                 
   For exammple: speciespartition species = SpeciesA: 1, SpeciesB: 2-.           
   Here, we name two species. SpeciesA is represented by a single sequence while 
   SpeciesB is represented by all remaining sequences in the matrix.             
   Each sequence is specified by its row index in the data matrix.               
                                                                                 
   As with ordinary partitioning you may define multiple species partitioning    
   scheme. You have to use command 'set speciespartition' to enable use of one of
   them.                                                                         
                                                                                 
   Currently defined Speciespartitions:                                          
                                                                                 
   Number  Speciespartition name        Number of species                        
   --------------------------------------------------------------------------    
                                                                                
   --------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Ss                                                                            
                                                                                 
   This command is used to start stepping-stone sampling, which is an efficient  
   and accurate method for estimating the marginal likelihood of the currently   
   specified model. It is considerably more accurate than the harmonic mean of   
   the likelihoods from a standard MCMC run on the model (calculated by the      
   'Sump' command) but it requires a separate MCMC-like run. To be more specific,
   stepping-stone sampling uses importance sampling to estimate each ratio in a  
   series of discrete steps bridging the posterior and prior distributions.      
   The importance distributions that are used are called power posterior distri- 
   butions, and are defined as prior*(likelihood^beta). By varying beta from 1 to
   0, we get a series of distributions that connect the posterior (beta = 1) to  
   the prior (beta = 0).                                                         
                                                                                 
   The power posterior distributions are sampled using MCMC. First, we start a   
   standard MCMC chain on the posterior distribution, and let it run until we    
   have reached the criterion specified by the 'Burninss' option. After this, we 
   step through the power posterior distributions until we reach the prior dis-  
   tribution. In each of the 'Nsteps' steps, we sample from a new power poster-  
   ior distribution with a distinct beta value. The beta values correspond to    
   'Nsteps' evenly spaced quantiles in a Beta distribution with the parameters   
   'Alpha' and 1.0. For the first sampling step, the beta value is equal to the  
   last quantile, i.e., it is close to 1.0. For each successive step, the beta   
   value takes on the value of the next quantile, in decreasing order, until it  
   reaches the value of 0.0. If you change value of 'FromPrior' from default 'No'
   to 'Yes' then the direction of power posterior change during SS analizes is   
   opposite to the one described above, i.e. we start from sampling prior and    
   finish close to posterior.                                                    
                                                                                 
   The 'Ss' procedure uses the same machinery as the standard 'Mcmc' algorithm,  
   and shares most of its parameters with the 'Mcmc' and 'Mcmcp' commands. All   
   'Mcmc' parameters, except those related to burnin, have the same meaning and  
   usage in the 'Ss' command as they have in the 'Mcmc' command. The 'Mcmc'      
   burnin parameters are used to set up burnin within each step. The 'Ss' command
   also uses its own burnin parameter, 'Burninss' (see below for details). The   
   'Ss' command also has its own parameters for specifying the number of steps   
   and the shape of the Beta distribution from which the beta values are computed
   (see below).                                                                  
                                                                                 
   Note that the 'Ngen' parameter of 'Mcmc' is used to set the maximum number of 
   generations processed, including both the burnin and the following steps in   
   the stepping-stone sampling phase. For instance, assume that 'Burninss' is set
   to '-1', 'Nsteps' to '49', 'Ngen' to '1000000' and 'Samplefreq' to '1000'.    
   We will then get 1,000 samples in total (1,000,000 / 1,000). These will fall  
   into 50 bins, one of which represents the burnin and is discarded. Each step  
   in the algorithm will thus be represented by 20 samples.                      
                                                                                 
   More information on 'Mcmc' parameters is available in the help for the 'Mcmc' 
   and 'Mcmcp' commands. Only the exclusive 'Ss' parameters are listed below.    
   These can only be set up using the 'Ss' command, while the parameters shared  
   with 'Mcmc' and 'Mcmcp' can also be set up using those commands.              
                                                                                 
   The correct usage is                                                          
                                                                                 
      ss <parameter>=<value> ... <parameter>=<value>                             
                                                                                 
   Note that a command:                                                          
                                                                                 
      ss <setting parameters shared with mcmc> <setting exclusive ss parameters> 
                                                                                 
   would be equivalent to executing two commands:                                
                                                                                 
     mcmcp <setting parameters shared with mcmc>;                                
     ss <setting exclusive ss parameters>;                                       
                                                                                 
   For more information on the stepping-stone algorithm, see:                    
                                                                                 
   Xie, W., P. O. Lewis, Y. Fan, L. Kuo, and M.-H. Chen. 2011. Improving marginal
      likelihood estimation for Bayesian phylogenetic model selection. Systematic
      Biology 60:150-160.                                                        
                                                                                 
   Available options:                                                            
   (NB: Only exclusive ss parameters listed here. For additional parameters, see 
        help on 'mcmc' or 'mcmcp'.                                               
                                                                                 
   Alpha        -- The beta values used in the stepping-stone sampling procedure 
                   correspond to evenly spaced quantiles from a Beta('Alpha',1.0)
                   distribution. The parameter 'Alpha' determines the skewness of
                   the beta values. If 'Alpha' is set to '1.0', the beta values  
                   would be spaced uniformly on the interval (0.0,1.0). However, 
                   better results are obtained if the beta values are skewed.    
                   Empirically, it was observed that 'Alpha' values in the range 
                   of 0.3 to 0.5 produce the most accurate results.              
   Burninss     -- Fixed number of samples discarded before sampling of the first
                   step starts. 'Burninss' can be specified using either a pos-  
                   itive or a negative number. If the number is positive, it is  
                   interpreted as the number of samples to discard as burnin. If 
                   the number is negative, its absolute value is interpreted as  
                   the length of the burnin in terms of the length of each of the
                   following steps in the stepping-stone algorithm. For instance,
                   a value of '-1' means that the length of the burnin is the    
                   same as the length of each of the subsequent steps.           
   Nsteps       -- Number of steps in the stepping-stone algorithm. Typically, a 
                   number above 30 is sufficient for accurate results.           
   FromPrior    -- If it is set to 'Yes', it indicates that in the first step we 
                   sample from the prior, with each consequtive step we sample   
                   closer to the posterior. 'No' indicates the opposite direction
                   of power posterior change, i.e. in the first step we sample   
                   close to the posterior, and with each consequtive step we     
                   sample closer to the prior.                                   
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter          Options               Current Setting                      
   --------------------------------------------------------                      
   Alpha              <number>              0.40
   BurninSS           <number>              -1
   Nsteps             <number>              50
   FromPrior           Yes/No               No                                   
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Ssp                                                                           
                                                                                 
   This command sets the parameters of the stepping-stone sampling               
   analysis without actually starting the chain. This command is identical       
   in all respects to Ss, except that the analysis will not start after          
   this command is issued. For more details on the options, check the help       
   menu for Ss.
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter          Options               Current Setting                      
   --------------------------------------------------------                      
   Alpha              <number>              0.40
   BurninSS           <number>              -1
   Nsteps             <number>              50
   FromPrior           Yes/No               No                                   
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Startvals                                                                     
                                                                                 
   Use this command to change the current values for parameters in your model.   
   These values will be used as the starting values in the next mcmc analysis.   
   The basic format is:                                                          
                                                                                 
      startvals <param>=(<value_1>,<value_2>,...,<value_n>)                      
                                                                                 
   for all substitution model parameters. The format is slightly different for   
   parameters that are written to a tree file:                                   
                                                                                 
      startvals <param>=<tree_name>                                              
                                                                                 
   This version of the command will look for a tree with the specified name      
   among the trees read in previously when parsing a tree block. The information 
   stored in that tree will be used to set the starting value of the parameter.  
   The parameters that are set using this mechanism include topology and branch  
   length parameters, as well as relaxed clock branch rates, cpp events and      
   cpp branch rate multipliers.                                                  
                                                                                 
   The above versions of the command will set the value for all runs and chains. 
   You can also set the value for an individual run and chain by using the format
                                                                                 
      startvals <param>(<run>,<chain>)=(<value_1>,...)                           
                                                                                 
   where <run> is the index of the run and <chain> the index of the chain. If    
   the run index is omitted, the values will be changed for all runs. Similarly, 
   if the chain index is omitted, all chains will be set to the specified value. 
   For example, if we wanted to set the values of the stationary frequency       
   parameter pi{1} to (0.1,0.1,0.4,0.4) for all chains in run 1, and to          
   (0.3,0.3,0.2,0.2) for chain 3 of run 2, we would use                          
                                                                                 
      startvals pi{1}(1,)=(0.1,0.1,0.4,0.4) pi{1}(2,3)=(0.3,0.3,0.2,0.2)         
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Sump                                                                          
                                                                                 
   During an MCMC analysis, MrBayes prints the sampled parameter values to one or
   more tab-delimited text files, one for each independent run in your analysis. 
   The command 'Sump' summarizes the information in this parameter file or these 
   parameter files. By default, the root of the parameter file name(s) is assumed
   to be the name of the last matrix-containing nexus file. MrBayes also remem-  
   bers the number of independent runs in the last analysis that you set up, re- 
   gardless of whether you actually ran it. For instance, if there were two in-  
   dependent runs, which is the initial setting when you read in a new matrix,   
   MrBayes will assume that there are two parameter files with the endings       
   '.run1.p' and '.run2.p'. You can change the root of the file names and the    
   number of runs using the 'Filename' and 'Nruns' settings.                     
                                                                                 
   When you invoke the 'Sump' command, three items are output: (1) a generation  
   plot of the likelihood values; (2) estimates of the marginal likelihood of    
   the model; and (3) a table with the mean, variance, and 95 percent credible   
   interval for the sampled parameters. All three items are output to screen.    
   The table of marginal likelihoods is also printed to a file with the ending   
   '.lstat' and the parameter table to a file with the ending '.pstat'. For some 
   model parameters, there may also be a '.mstat' file.                          
                                                                                 
   When running 'Sump' you typically want to discard a specified number or       
   fraction of samples from the beginning of the chain as the burn in. This is   
   done using the same mechanism used by the 'mcmc' command. That is, if you     
   run an mcmc analysis with a relative burn in of 25 % of samples for con-     
   vergence diagnostics, then the same burn in will be used for a subsequent     
   sump command, unless a different burn in is specified. That is, issuing       
                                                                                 
   sump                                                                          
                                                                                 
   immediately after 'mcmc', will result in using the same burn in settings as   
   for the 'mcmc' command. All burnin settings are reset to default values every 
   time a new matrix is read in, namely relative burnin ('relburnin=yes') with   
   25 % of samples discarded ('burninfrac = 0.25').                             
                                                                                 
   Options:                                                                      
                                                                                 
   Relburnin    -- If this option is set to 'Yes', then a proportion of the      
                   samples will be discarded as burnin when calculating summary  
                   statistics. The proportion to be discarded is set with        
                   'Burninfrac' (see below). When the 'Relburnin' option is set  
                   to 'No', then a specific number of samples is discarded       
                   instead. This number is set by 'Burnin' (see below). Note that
                   the burnin setting is shared across the 'sumt', 'sump', and   
                   'mcmc' commands.                                              
   Burnin       -- Determines the number of samples (not generations) that will  
                   be discarded when summary statistics are calculated. The      
                   value of this option is only applicable when 'Relburnin' is   
                   set to 'No'.                                                  
   Burninfrac   -- Determines the fraction of samples that will be discarded when
                   summary statistics are calculated. The setting only takes     
                   effect if 'Relburnin' is set to 'Yes'.                        
   Nruns        -- Determines how many '.p' files from independent analyses that 
                   will be summarized. If Nruns > 1 then the names of the files  
                   are derived from 'Filename' by adding '.run1.p', '.run2.p',   
                   etc. If Nruns=1, then the single file name is obtained by     
                   adding '.p' to 'Filename'.                                    
   Filename     -- The name of the file to be summarized. This is the base of the
                   file name to which endings are added according to the current 
                   setting of the 'Nruns' parameter. If 'Nruns' is 1, then only  
                   '.p' is added to the file name. Otherwise, the endings will   
                   be '.run1.p', '.run2.p', etc.                                 
   Outputname   -- Base name of the file(s) to which 'Sump' results will be      
                   printed.                                                      
   Hpd          -- Determines whether credibility intervals will be given as the 
                   region of Highest Posterior Density ('Yes') or as the interval
                   containing the median 95 % of sampled values ('No').         
   Minprob      -- Determines the minimum probability of submodels to be included
                   in summary statistics. Only applicable to models that explore 
                   submodel spaces, like 'nst=mixed' and 'aamodelpr=mixed'.      
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter       Options                  Current Setting                      
   --------------------------------------------------------                      
   Relburnin       Yes/No                   Yes                                   
   Burnin          <number>                 0                                   
   Burninfrac      <number>                 0.25                               
   Nruns           <number>                 2                                   
   Filename        <name>                   temp<.run<i>.p>
   Outputname      <name>                   temp<.pstat etc>
   Hpd             Yes/No                   Yes                                   
   Minprob         <number>                 0.050                               
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Sumss                                                                         
                                                                                 
   This command summarizes results of stepping stone analyses. It is a tool to   
   investigate the obtained results, and to help find the proper step burn-in.   
   To get more help information on stepping-stone analyses, use 'help ss'.       
                                                                                 
   During stepping-stone analysis, MrBayes collects the sampled likelihoods in   
   order to estimate the marginal likelihood at the end. It also prints the sam- 
   pled parameter values to one or more tab-delimited text files, one for each   
   independent run in your analysis. The command 'Sumss' summarizes likelihood   
   values stored in these parameter files and calculates marginal likelihood es- 
   timates. The names of the files that are summarized are exactly the same as   
   the names of the files used for the 'sump' command. In fact, the 'filename'   
   setting is a shared setting for the 'sump' and 'sumss' commands. That is, if  
   you change the setting in one of the commands, it would change the setting in 
   the other command as well.                                                    
                                                                                 
   When you invoke the 'Sumss' command, three items are output: (1) 'Step contri-
   bution table' - summarizes the contribution of each step to the overall esti- 
   mate; (2) 'Step plot' - plot of the likelihood values for the initial burn-in 
   phase or a chosen step in the stepping-stone algorithm; (3) 'Joined plot' -   
   summarizes sampling across all steps in the algorithm.                        
                                                                                 
   Step contribution table                                                       
   The printed table is similar to the one output to the .ss file. The main pur- 
   pose of the table is to summarize marginal likelihood for different values of 
   the step burn-in after the stepping stone  analysis has finished. The burn-in 
   is controlled by the 'Relburnin', 'Burnin' and 'Burninfrac' settings.         
   Note that during stepping-stone analyses, step contributions to marginal      
   likelihood are calculated based on all generations excluding burn-in. 'Sumss' 
   on the other hand makes estimates based only on the sampled generations. This 
   may lead to slight difference in results compared to the one printed to the   
   .ss file.                                                                     
                                                                                 
   Step plot                                                                     
   The main objective of the plot is to provide a close look at a given step in  
   the analysis. Which step is printed here is defined by the 'Steptoplot' set-  
   ting. The plot could be used to inspect if the chosen step burn-in is appro-  
   priate for the given step. It could also be used to check if the initial burn-
   in phase has converged. Note that the amount of discarded samples is controled
   by the 'Discardfrac' setting, and not by the ordinary burn-in settings.       
                                                                                 
   Joined plot                                                                   
   Different steps sample from different power posterior distributions. When we  
   switch from one distribution to another, it takes some number of generations  
   before the chain settles at the correct stationary distribution. This lag is  
   called a 'temperature lag' and if the corresponding samples are not removed,  
   it will result in a biased estimate. It is difficult to determine the lag be- 
   forehand, but MrBayes allows you to explore different step burn-in settings   
   after you have finished the stepping-stone algorithm, without having to rerun 
   the whole analysis. The 'Joined plot' helps to facilitate the choice of the   
   right step burn-in. The plot summarizes samples across all steps and gives you
   a quick overview of the whole analysis.                                       
                                                                                 
   Specifically, the following procedure is used to obtain the joined plot. Each 
   step has the same number N of samples taken. We number each sample 1 to N     
   within steps according to the order in which the samples are taken. The first 
   sample in each step is numbered 1, and the last sample is N. For each number i
   in [1,..., N], we sum up log likelihoods for all samples numbered i across all
   steps. The joined plot is a graph of the step number versus the normalized    
   sums we get in the procedure describe above. This directly visualizes the tem-
   perature lag and allows you to select the appropriate step burn-in.           
                                                                                 
   Ideally, after you discard the appropriate step burn-in, the graph should     
   appear as white noise around the estimated value. If you see an increasing or 
   decreasing tendency in the beginning of the graph, you should increase the    
   step burn-in. If you see an increasing or decreasing tendency across the whole
   graph, then the initial burn-in phase was not long enough. In this case, you  
   need to rerun the analysis with a longer initial burn-in.                     
                                                                                 
   To make it easier to observe tendencies in the plotted graph you can choose   
   different levels of curve smoothing. If 'Smoothing' is set to k, it means that
   for each step i we take an average over step i and k neighboring samples in   
   both directions, i.e., the k-smoothed estimate for step i is an average over  
   values for steps [i-k,...,i+k].                                               
                                                                                 
                                                                                 
   Options:                                                                      
                                                                                 
   Allruns      -- If set to 'Yes', it forces all runs to be printed on the same 
                   graph when drawing joined and step plots. If set to 'No', each
                   run is printed on a separat plot.                             
   Askmore      -- Long analyses may produce huge .p files. Reading in them may  
                   take several minutes. If you want to investigate different    
                   aspects of your analyses, it could be very inconvenient to    
                   wait for several minutes each time you want to get a new sum- 
                   mary for different settings. If you set 'Askmore' to 'YES',   
                   sumss will read .p files only once. After responding to the   
                   original query, it will interactivaly ask you if you wish to  
                   produce more tables and plots for different settings of       
                   'Burnin' or 'Smoothing' (see below).                          
   Relburnin    -- If this option is set to 'Yes', then a proportion of the      
                   samples from each step will be discarded as burnin when calcu-
                   lsting summary statistics. The proportion to be discarded is  
                   set with 'Burninfrac' (see below). When the 'Relburnin' option
                   is set to 'No', then a specific number of samples is discarded
                   instead. This number is set by 'Burnin'. Note that the burnin 
                   settings --- 'Relburnin', 'Burnin', and 'Burninfrac' --- are  
                   shared across the 'sumt', 'sump', 'sumss' and 'mcmc' commands.
   Burnin       -- Determines the number of samples (not generations) that will  
                   be discarded from each step when summary statistics are calcu-
                   lated. The value of this option is only applicable when       
                   'Relburnin' is set to 'No'.                                   
   Burninfrac   -- Determines the fraction of samples that will be discarded from
                   each step when summary statistics are calculated. The setting 
                   only takes effect if 'Relburnin' is set to 'Yes'.             
   Discardfrac  -- Determines the fraction of samples that will be discarded when
                   a step plot is printed. It is similar to the 'Burninfrac' set-
                   ting, but unlike 'Burninfrac' it is used only for better vis- 
                   ualization of the step plot. It has no effect on the number of
                   samples discarded during marginal likelihood computation.     
   Filename     -- The name of the file to be summarized. This is the base of the
                   file name to which endings are added according to the current 
                   setting of the 'Nruns' parameter. If 'Nruns' is 1, then only  
                   '.p' is added to the file name. Otherwise, the endings will   
                   be '.run1.p', '.run2.p', etc. Note that the 'Filename' setting
                   is shared with 'sump' command.                                
   Nruns        -- Determines how many '.p' files from independent analyses that 
                   will be summarized. If Nruns > 1 then the names of the files  
                   are derived from 'Filename' by adding '.run1.p', '.run2.p',   
                   etc. If Nruns=1, then the single file name is obtained by     
                   adding '.p' to 'Filename'.                                    
   Steptoplot   -- Defines which step will be printed in the step plot.If the    
                   value is set to 0, then the initial sample from the posterior 
                   will be used.                                                 
   Smoothing    -- Determines smoothing of the joined plot (see above). A value  
                   equal to 0 results in no smoothing.                           
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter       Options                  Current Setting                      
   --------------------------------------------------------                      
   Allruns         Yes/No                   Yes                                   
   Askmore         Yes/No                   Yes                                   
   Relburnin       Yes/No                   Yes                                   
   Burnin          <number>                 0                                   
   Burninfrac      <number>                 0.25                               
   Discardfrac     <number>                 0.80                               
   Filename        <name>                   temp<.run<i>.p>
   Nruns           <number>                 2                                   
   Steptoplot      <number>                 0                                   
   Smoothing       <number>                 0                                   
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Sumt                                                                          
                                                                                 
   This command is used to produce summary statistics for trees sampled during   
   a Bayesian MCMC analysis. You can either summarize trees from one individual  
   analysis, or trees coming from several independent analyses. In either case,  
   all the sampled trees are read in and the proportion of the time any single   
   taxon bipartition (split) is found is counted. The proportion of the time that
   the bipartition is found is an approximation of the posterior probability of  
   the bipartition. (Remember that a taxon bipartition is defined by removing a  
   branch on the tree, dividing the tree into those taxa to the left and right   
   of the removed branch. This set is called a taxon bipartition.) The branch    
   length of the bipartition is also recorded, if branch lengths have been saved 
   to file. The result is a list of the taxon bipartitions found, the frequency  
   with which they were found, the posterior probability of the bipartition      
   and, the mean and variance of the branch lengths or node depths, and various  
   other statistics.                                                             
                                                                                 
   The key to the partitions is output to a file with the suffix '.parts'. The   
   summary statistics pertaining to bipartition probabilities are output to a    
   file with the suffix '.tstat', and the statistics pertaining to branch or node
   parameters are output to a file with the suffix '.vstat'.                     
                                                                                 
   A consensus tree is also printed to a file with the suffix '.con.tre' and     
   printed to the screen as a cladogram, and as a phylogram if branch lengths    
   have been saved. The consensus tree is either a 50 percent majority rule tree 
   or a majority rule tree showing all compatible partitions. If branch lengths  
   have been recorded during the run, the '.con.tre' file will contain a consen- 
   sus tree with branch lengths and interior nodes labelled with support values. 
   By default, the consensus tree will also contain other summary information in 
   a format understood by the program 'FigTree'. To use a simpler format under-  
   stood by other tree-drawing programs, such as 'TreeView', set 'Conformat' to  
   'Simple'.                                                                     
                                                                                 
   MrBayes alo produces a file with the ending ".trprobs" that contains a list 
   of all the trees that were found during the MCMC analysis, sorted by their    
   probabilities. This list of trees can be used to construct a credible set of  
   trees. For example, if you want to construct a 95 percent credible set of     
   trees, you include all of those trees whose cumulative probability is less    
   than or equal to 0.95. You have the option of displaying the trees to the     
   screen using the "Showtreeprobs" option. The default is to not display the  
   trees to the screen; the number of different trees sampled by the chain can   
   be quite large. If you are analyzing a large set of taxa, you may actually    
   want to skip the calculation of tree probabilities entirely by setting        
   'Calctreeprobs' to 'No'.                                                      
                                                                                 
   When calculating summary statistics you probably want to skip those trees that
   were sampled in the initial part of the run, the so-called burn-in period. The
   number of skipped samples is controlled by the 'Relburnin', 'Burnin', and     
   'Burninfrac' settings, just as for the 'Mcmc' command. Since version 3.2.0,   
   the burn-in settings are shared across the 'Sumt', 'Sump' and 'Mcmc' commands.
   That is, changing the burn-in setting for one command will change the settings
   for subsequent calls to any of the other commands.                            
                                                                                 
   If you are summarizing the trees sampled in several independent analyses,     
   such as those resulting from setting the 'Nruns' option of the 'Mcmc' command 
   to a value larger than 1, MrBayes will also calculate convergence diagnostics 
   for the sampled topologies and branch lengths. These values can help you      
   determine whether it is likely that your chains have converged.               
                                                                                 
   The 'Sumt' command expands the 'Filename' according to the current values of  
   the 'Nruns' and 'Ntrees' options. For instance, if both 'Nruns' and 'Ntrees'  
   are set to 1, 'Sumt' will try to open a file named '<Filename>.t'. If 'Nruns' 
   is set to 2 and 'Ntrees' to 1, then 'Sumt' will open two files, the first     
   named '<Filename>.run1.t' and the second '<Filename>.run2.t', etc. By default,
   the 'Filename' option is set such that 'Sumt' automatically summarizes all the
   results from your immediately preceding 'Mcmc' command. You can also use the  
   'Sumt' command to summarize tree samples in older analyses. If you want to do 
   that, remember to first read in a matrix so that MrBayes knows what taxon     
   names to expect in the trees. Then set the 'Nruns', 'Ntrees' and 'Filename'   
   options appropriately if they differ from the MrBayes defaults.               
                                                                                 
   Options:                                                                      
                                                                                 
   Relburnin     -- If this option is set to YES, then a proportion of the       
                    samples will be discarded as burnin when calculating summary 
                    statistics. The proportion to be discarded is set with       
                    Burninfrac (see below). When the Relburnin option is set to  
                    NO, then a specific number of samples is discarded instead.  
                    This number is set by Burnin (see below). Note that the      
                    burnin setting is shared across the 'sumt', 'sump', and      
                    'mcmc' commands.                                             
   Burnin        -- Determines the number of samples (not generations) that will 
                    be discarded when summary statistics are calculated. The     
                    value of this option is only relevant when Relburnin is set  
                    to NO.                                                       
   BurninFrac    -- Determines the fraction of samples that will be discarded    
                    when summary statistics are calculated. The value of this    
                    option is only relevant when Relburnin is set to YES.        
                    Example: A value for this option of 0.25 means that 25% of  
                    the samples will be discarded.                               
   Nruns         -- Determines how many '.t' files from independent analyses that
                    will be summarized. If Nruns > 1 then the names of the files 
                    are derived from 'Filename' by adding '.run1.t', '.run2.t',  
                    etc. If Nruns=1 and Ntrees=1 (see below), then only '.t' is  
                    added to 'Filename'.                                         
   Ntrees        -- Determines how many trees there are in the sampled model. If 
                    'Ntrees' > 1 then the names of the files are derived from    
                    'Filename' by adding '.tree1.t', '.tree2.t', etc. If there   
                    are both multiple trees and multiple runs, the filenames will
                    be '<Filename>.tree1.run1.t', '<Filename>.tree1.run2.t', etc.
   Filename      -- The name of the file(s) to be summarized. This is the base of
                    the file name, to which endings are added according to the   
                    current settings of the 'Nruns' and 'Ntrees' options.        
   Minpartfreq   -- The minimum probability of partitions to include in summary  
                    statistics.                                                  
   Contype       -- Type of consensus tree. 'Halfcompat' results in a 50% major-
                    ity rule tree, 'Allcompat' adds all compatible groups to such
                    a tree.                                                      
   Conformat     -- Format of consensus tree. The 'Figtree' setting results in a 
                    consensus tree formatted for the program FigTree, with rich  
                    summary statistics. The 'Simple' setting results in a simple 
                    consensus tree written in a format read by a variety of pro- 
                    grams.                                                       
   Outputname    -- Base name of the file(s) to which 'sumt' results will be     
                    printed. The default is the same as 'Filename'.              
   Calctreeprobs -- Determines whether tree probabilities should be calculated.  
   Showtreeprobs -- Determines whether tree probabilities should be displayed on 
                    screen.                                                      
   Hpd           -- Determines whether credibility intervals will be given as the
                    region of Highest Posterior Density ('Yes') or as the inter- 
                    val containing the median 95 % of sampled values ('No').    
                                                                                 
   Current settings:                                                             
                                                                                 
   Parameter       Options                  Current Setting                      
   --------------------------------------------------------                      
   Relburnin       Yes/No                   Yes                                   
   Burnin          <number>                 0                                   
   Burninfrac      <number>                 0.25                               
   Nruns           <number>                 2                                   
   Ntrees          <number>                 1                                   
   Filename        <name>                   temp<.run<i>.t>
   Minpartfreq     <number>                 0.10                               
   Contype         Halfcompat/Allcompat     Halfcompat
   Conformat       Figtree/Simple           Figtree                                   
   Outputname      <name>                   temp<.parts etc>
   Calctreeprobs   Yes/No                   Yes                                   
   Showtreeprobs   Yes/No                   No                                   
   Hpd             Yes/No                   Yes                                   
                                                                                 
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Taxastat                                                                      
                                                                                 
   This command shows the status of all the taxa. The correct usage is           
                                                                                 
      taxastat                                                                   
                                                                                 
   After typing "taxastat", the taxon number, name, and whether it is          
   excluded or included are shown.                                               
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Taxset                                                                        
                                                                                 
   This command defines a taxon set. The format for the taxset command           
   is                                                                            
                                                                                 
      taxset <name> = <taxon names or numbers>                                   
                                                                                 
   For example, "taxset apes = Homo Pan Gorilla Orang gibbon" defines a        
   taxon set called "apes" that includes five taxa (namely, apes).             
   You can assign up to 30 taxon sets. This option is best used                  
   not from the command line but rather as a line in the mrbayes block           
   of a file.                                                                    
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Unlink                                                                        
                                                                                 
   This command unlinks model parameters across partitions of the data. The      
   correct usage is:                                                             
                                                                                 
      unlink <parameter name> = (<all> or <partition list>)                      
                                                                                 
   A little background is necessary to understand this command. Upon exe-        
   cution of a file, a default partition is set up. This partition refer-        
   enced either by its name ("default") or number (0). If your data are        
   all of one type, then this default partition does not actually divide up      
   your characters. However, if your datatype is mixed, then the default         
   partition contains as many divisions as there are datatypes in your           
   character matrix. Of course, you can also define other partitions, and        
   switch among them using the set command ("set partition=<name/number>").    
   Importantly, you can also assign model parameters to individual part-         
   itions or to groups of them using the "applyto" option in lset and          
   prset. When the program attempts to perform an analysis, the model is         
   set for individual partitions. If the same parameter applies to differ-       
   partitions and if that parameter has the same prior, then the program         
   will link the parameters: that is, it will use a single value for the         
   parameter. The program's default, then, is to strive for parsimony.           
   However, there are lots of cases where you may want unlink a parameter        
   across partitions. For example, you may want a different transition/          
   transversion rate ratio to apply to different partitions. This command        
   allows you to unlink the parameters, or to make them different across         
   partitions. The converse of this command is "link", which links to-         
   gether parameters that were previously told to be different. The list         
   of parameters that can be unlinked includes:                                  
                                                                                 
      Tratio          -- Transition/transversion rate ratio                      
      Revmat          -- Substitution rates of GTR model                         
      Omega           -- Nonsynonymous/synonymous rate ratio                     
      Statefreq       -- Character state frequencies                             
      Shape           -- Gamma/LNorm shape parameter                             
      Pinvar          -- Proportion of invariable sites                          
      Correlation     -- Correlation parameter of autodiscrete gamma             
      Ratemultiplier  -- Rate multiplier for partitions                          
      Switchrates     -- Switching rates for covarion model                      
      Topology        -- Topology of tree                                        
      Brlens          -- Branch lengths of tree                                  
      Speciationrate  -- Speciation rates for birth-death process                
      Extinctionrate  -- Extinction rates for birth-death process                
      Popsize         -- Population size for coalescence process                 
      Growthrate      -- Growth rate of coalescence process                      
      Aamodel         -- Aminoacid rate matrix                                   
      Cpprate         -- Rate of Compound Poisson Process (CPP)                  
      Cppmultdev      -- Standard dev. of CPP rate multipliers (log scale)       
      Cppevents       -- CPP events                                              
      TK02var         -- Variance increase in TK02 relaxed clock model           
      Igrvar          -- Variance increase in IGR relaxed clock model            
      Mixedvar        -- Variance increase in Mixed relaxed clock model          
                                                                                 
   For example,                                                                  
                                                                                 
      unlink shape=(all)                                                         
                                                                                 
   unlinks the gamma/lnorm shape parameter across all partitions of the data.    
   You can use "showmodel" to see the current linking status of the            
   characters.                                                                   
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Version                                                                       
                                                                                 
   This command shows the release version of the program.                        
   ---------------------------------------------------------------------------   
                                                                                 
   ***************************************************************************   
   *                                                                         *   
   *  3. 'Data' or 'tree' block commands (in #NEXUS file)                    *   
   *                                                                         *   
   ***************************************************************************   
                                                                                 
   ---------------------------------------------------------------------------   
   Begin                                                                         
                                                                                 
   This command is used to format data or commands in the program. The correct   
   usage is                                                                      
                                                                                 
      begin <data or mrbayes>;                                                   
                                                                                 
   The two valid uses of the "begin" command, then, are                        
                                                                                 
      begin data;                                                                
      begin mrbayes;                                                             
                                                                                 
   The "data" specifier is used to specify the beginning of a data block; your 
   character data should follow. For example, the following is an example of     
   a data block for four taxa and ten DNA sites:                                 
                                                                                 
      begin data;                                                                
         dimensions ntax=4 nchar=10;                                             
         format datatype=dna;                                                    
         matrix                                                                  
         taxon_1  AACGATTCGT                                                     
         taxon_2  AAGGATTCCA                                                     
         taxon_3  AACGACTCCT                                                     
         taxon_4  AAGGATTCCT                                                     
         ;                                                                       
      end;                                                                       
                                                                                 
   The other commands -- dimensions, format, and matrix -- are discussed         
   in the appropriate help menu. The only thing to note here is that the         
   block begins with a "begin data" command. The "mrbayes" command is        
   used to enter commands specific to the MrBayes program into the file.         
   This allows you to automatically process commands on execution of the         
   program. The following is a simple mrbayes block:                             
                                                                                 
      begin mrbayes;                                                             
         charset first  = 1-10\3;                                               
         charset second = 2-10\3;                                               
         charset third  = 3-10\3;                                               
      end;                                                                       
                                                                                 
   This mrbayes block sets off the three "charset" commands, used to           
   predefine some blocks of characters. The mrbayes block can be very useful.    
   For example, in this case, it would save you the time of typing the char-     
   acter sets each time you executed the file. Also, note that every             
   "begin <data or mrbayes>" command ends with an "end". Finally, you can    
   have so-called foreign blocks in the file. An example of a foreign block      
   would be "begin paup". The program will simply skip this block. This is     
   useful because it means that you can use the same file for MrBayes, PAUP*     
   or MacClade (although it isn't clear why you would want to use those other    
   programs).                                                                    
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Dimensions                                                                    
                                                                                 
   This command is used in a data block to define the number of taxa and         
   characters. The correct usage is                                              
                                                                                 
      dimensions ntax=<number> nchar=<number>                                    
                                                                                 
   The dimensions must be the first command in a data block. The following       
   provides an example of the proper use of this command:                        
                                                                                 
      begin data;                                                                
         dimensions ntax=4 nchar=10;                                             
         format datatype=dna;                                                    
         matrix                                                                  
         taxon_1  AACGATTCGT                                                     
         taxon_2  AAGGATTCCA                                                     
         taxon_3  AACGACTCCT                                                     
         taxon_4  AAGGATTCCT                                                     
         ;                                                                       
      end;                                                                       
                                                                                 
   Here, the dimensions command tells MrBayes to expect a matrix with four       
   taxa and 10 characters.                                                       
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   End                                                                           
                                                                                 
   This command is used to terminate a data or mrbayes block. The correct        
   usage is                                                                      
                                                                                 
      end;                                                                       
                                                                                 
   For more information on this, check the help for the "begin" command.       
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Endblock                                                                      
                                                                                 
   This is an older, deprecated version of "End", see that command.            
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Format                                                                        
                                                                                 
   This command is used in a data block to define the format of the char-        
   acter matrix. The correct usage is                                            
                                                                                 
      format datatype=<name> ... <parameter>=<option>                            
                                                                                 
   The format command must be the second command in a data block. The following  
   provides an example of the proper use of this command:                        
                                                                                 
      begin data;                                                                
         dimensions ntax=4 nchar=10;                                             
         format datatype=dna gap=-;                                              
         matrix                                                                  
         taxon_1  AACGATTCGT                                                     
         taxon_2  AAGGAT--CA                                                     
         taxon_3  AACGACTCCT                                                     
         taxon_4  AAGGATTCCT                                                     
         ;                                                                       
      end;                                                                       
                                                                                 
   Here, the format command tells MrBayes to expect a matrix with DNA char-      
   acters and with gaps coded as "-".                                          
                                                                                 
   The following are valid options for format:                                   
                                                                                 
   Datatype   -- This parameter MUST BE INCLUDED in the format command. More-    
                 over, it must be the first parameter in the line. The           
                 datatype command specifies what type of characters are          
                 in the matrix. The following are valid options:                 
                    Datatype = Dna: DNA states (A,C,G,T,R,Y,M,K,S,W,H,B,         
                               V,D,N)                                            
                    Datatype = Rna: DNA states (A,C,G,U,R,Y,M,K,S,W,H,B,         
                               V,D,N)                                            
                    Datatype = Protein: Amino acid states (A,R,N,D,C,Q,E,        
                               G,H,I,L,K,M,F,P,S,T,W,Y,V)                        
                    Datatype = Restriction: Restriction site (0,1) states        
                    Datatype = Standard: Morphological (0,1) states              
                    Datatype = Continuous: Real number valued states             
                    Datatype = Mixed(<type>:<range>,...,<type>:<range>): A       
                               mixture of the above datatypes. For example,      
                               "datatype=mixed(dna:1-100,protein:101-200)"     
                               would specify a mixture of DNA and amino acid     
                               characters with the DNA characters occupying      
                               the first 100 sites and the amino acid char-      
                               acters occupying the last 100 sites.              
                                                                                 
   Interleave -- This parameter specifies whether the data matrix is in          
                 interleave format. The valid options are "Yes" or "No",     
                 with "No" as the default. An interleaved matrix looks like    
                                                                                 
                    format datatype=dna gap=- interleave=yes;                    
                    matrix                                                       
                    taxon_1  AACGATTCGT                                          
                    taxon_2  AAGGAT--CA                                          
                    taxon_3  AACGACTCCT                                          
                    taxon_4  AAGGATTCCT                                          
                                                                                 
                    taxon_1  CCTGGTAC                                            
                    taxon_2  CCTGGTAC                                            
                    taxon_3  ---GGTAG                                            
                    taxon_4  ---GGTAG                                            
                    ;                                                            
                                                                                 
   Gap        -- This parameter specifies the format for gaps. Note that         
                 gap character can only be a single character and that it        
                 cannot correspond to a standard state (e.g., A,C,G,T,R,Y,       
                 M,K,S,W,H,B,V,D,N for nucleotide data).                         
                                                                                 
   Missing    -- This parameter specifies the format for missing data. Note      
                 that the missing character can only be a single character and   
                 cannot correspond to a standard state (e.g., A,C,G,T,R,Y,       
                 M,K,S,W,H,B,V,D,N for nucleotide data). This is often an        
                 unnecessary parameter to set because many data types, such      
                 as nucleotide or amino acid, already have a missing char-       
                 acter specified. However, for morphological or restriction      
                 site data, "missing=?" is often used to specify ambiguity     
                 or unobserved data.                                             
                                                                                 
   Matchchar  -- This parameter specifies the matching character for the         
                 matrix. For example,                                            
                                                                                 
                    format datatype=dna gap=- matchchar=.;                       
                    matrix                                                       
                    taxon_1  AACGATTCGT                                          
                    taxon_2  ..G...--CA                                          
                    taxon_3  .....C..C.                                          
                    taxon_4  ..G.....C.                                          
                    ;                                                            
                                                                                 
                 is equivalent to                                                
                                                                                 
                    format datatype=dna gap=-;                                   
                    matrix                                                       
                    taxon_1  AACGATTCGT                                          
                    taxon_2  AAGGAT--CA                                          
                    taxon_3  AACGACTCCT                                          
                    taxon_4  AAGGATTCCT                                          
                    ;                                                            
                                                                                 
   The only non-standard NEXUS format option is the use of the "mixed",        
   "restriction", "standard" and "continuous" datatypes. Hence, if         
   you use any of these datatype specifiers, a program like PAUP* or             
   MacClade will report an error (as they should because MrBayes is not          
   strictly NEXUS compliant).                                                    
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Matrix                                                                        
                                                                                 
   This command specifies the actual data for the phylogenetic analysis.         
   The character matrix should follow the dimensions and format commands         
   in a data block. The matrix can have all of the characters for a taxon        
   on a single line:                                                             
                                                                                 
      begin data;                                                                
         dimensions ntax=4 nchar=10;                                             
         format datatype=dna gap=-;                                              
         matrix                                                                  
         taxon_1  AACGATTCGT                                                     
         taxon_2  AAGGAT--CA                                                     
         taxon_3  AACGACTCCT                                                     
         taxon_4  AAGGATTCCT                                                     
         ;                                                                       
      end;                                                                       
                                                                                 
   or be in "interleaved" format:                                              
                                                                                 
      begin data;                                                                
         dimensions ntax=4 nchar=20;                                             
         format datatype=dna gap=- interleave=yes;                               
         matrix                                                                  
         taxon_1  AACGATTCGT                                                     
         taxon_2  AAGGAT--CA                                                     
         taxon_3  AACGACTCCT                                                     
         taxon_4  AAGGATTCCT                                                     
                                                                                 
         taxon_1  TTTTCGAAGC                                                     
         taxon_2  TTTTCGGAGC                                                     
         taxon_3  TTTTTGATGC                                                     
         taxon_4  TTTTCGGAGC                                                     
         ;                                                                       
      end;                                                                       
                                                                                 
   Note that the taxon names must not have spaces. If you really want to         
   indicate a space in a taxon name (perhaps between a genus and species         
   name), then you might use an underline ("_"). There should be at            
   least a single space after the taxon name, separating the name from           
   the actual data on that line. There can be spaces between the char-           
   acters.                                                                       
                                                                                 
   If you have mixed data, then you specify all of the data in the same          
   matrix. Here is an example that includes two different data types:            
                                                                                 
      begin data;                                                                
         dimensions ntax=4 nchar=20;                                             
         format datatype=mixed(dna:1-10,standard:21-30) interleave=yes;          
         matrix                                                                  
         taxon_1  AACGATTCGT                                                     
         taxon_2  AAGGAT--CA                                                     
         taxon_3  AACGACTCCT                                                     
         taxon_4  AAGGATTCCT                                                     
                                                                                 
         taxon_1  0001111111                                                     
         taxon_2  0111110000                                                     
         taxon_3  1110000000                                                     
         taxon_4  1000001111                                                     
         ;                                                                       
      end;                                                                       
                                                                                 
   The matrix command is terminated by a semicolon.                              
                                                                                 
   Finally, just a note on data presentation. It is much easier for others       
   to (1) understand your data and (2) repeat your analyses if you make          
   your data clean, comment it liberally (using the square brackets), and        
   embed the commands you used in a publication in the mrbayes block.            
   Remember that the data took a long time for you to collect. You might         
   as well spend a little time making the data file look nice and clear to       
   any that may later request the data for further analysis.                     
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Taxlabels                                                                     
                                                                                 
   This command defines taxon labels. It could be used within taxa block.        
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Translate                                                                     
                                                                                 
   This command is used by MrBayes to specify the mapping between taxon names    
   and taxon numbers in a Nexus tree file. For instance,                         
                                                                                 
      translate                                                                  
         1 Homo,                                                                 
         2 Pan,                                                                  
         3 Gorilla,                                                              
         4 Hylobates;                                                            
                                                                                 
   establishes that the taxon labeled 1 in the trees that follow is Homo, the    
   taxon labeled 2 is Pan, etc.                                                  
   ---------------------------------------------------------------------------   
   ---------------------------------------------------------------------------   
   Tree                                                                          
                                                                                 
   This command is used by MrBayes to write trees to a nexus tree file. Trees    
   are written in the Newick format. For instance,                               
                                                                                 
      tree ((1,2),3,4);                                                          
                                                                                 
   describes an unrooted tree with taxa 1 and 2 being more closely related to    
   each other than to taxa 3 and 4. If branch lengths are saved to file, they    
   are given after a colon sign immediately following the terminal taxon or the  
   interior node they refer to. An example of an unrooted tree with branch       
   lengths is:                                                                   
                                                                                 
      tree ((1:0.064573,2:0.029042):0.041239,3:0.203988,4:0.187654);             
                                                                                 
   Trees that are rooted (clock trees) are written with a basal dichotomy        
   instead of a basal trichotomy. If the tree described above had been rooted    
   on the branch leading to taxon 4, it would have been represented as:          
                                                                                 
      tree (((1,2),3),4);                                                        
                                                                                 
   ---------------------------------------------------------------------------   
