MrBayes 3.2 release todo-list
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DONE
 - Debugging branch fredrik: new format, plot, sumt, sump -- Fredrik
 - Merge fredrik with trunk -- Maxim
 - Modify sumt output to have separate table of splits -- Fredrik
 - Debug and polish plot -- Fredrik
 - Debug and polish comparetree -- Fredrik
 - Check coalescent prior (LnCoalescencePriorPr) -- Maxim
 - Check that nothing lost between cvs and svn root of trunk -- Maxim
 - Go through all bug reports on SourceForge -- Maxim
 - Build test files that exercise most models in MrBayes 3.2 -- Maxim and Fredrik
 - Make sure FigTree can read the consensus tree (FIGTREE format) -- Maxim
 - Correct sumt when number of trees > 1 -- Fredrik
 - Change addresses in all source files -- Fredrik
 - Polish sumt, sump -- Fredrik
 - Check implementation of HPD and help info for that -- Fredrik
 - Updated version of tutorial -- Fredrik
 - Set up visual studio project for beagle version of mrbayes -- Fredrik
 - Finish initial Beagle implementation -- Fredrik
 - Check birth-death (LnBirthDeathPriorPr) prior -- Fredrik
 - Make sumt summarize cpp events per branch (mean, range, HPD on number of events) and branch rates (same thing) -- Maxim
 - Move web site to SourceForge -- Maxim
 - Add tex of Tutorial v 3.2 to documentation folder -- Fredrik
 - Add beaglebayes project to svn beagle2 branch -- Fredrik
 - Delete branches fredrik and beagle -- Fredrik
 - Translate manual to Latex, incorporate new version of tutorial, commit to svn -- Maxim
 - Merge from trunk to beagle2 -- Fredrik
 - Delete all the old code used by likelihood calculators and update CondLikeUp in beagle2 -- Fredrik
 - Make sure beagle CPU version runs for some simple model -- Fredrik
 - Add SSE versions of all cond like down, up, root, scaler and Likelihood functions -- Maxim
 - Add shortcut to SSE versions of CondLikeDown -- Maxim
 - Finish branch beagle2 -- Fredrik
 - Merge branch beagle2 to trunk -- Fredrik & Maxim
 - Changing nruns & nchains  -- Maxim
 - Update print info about consensus phylogram (average or median node) -- Fredrik
 - Finish Beagle coding -- Fredrik & Maxim
 - Make Standard computation work in beagle2 -- Fredrik
 - Test all topology proposals with constraints -- Fredrik
 - Metropolize all tree proposals -- Fredrik
 - Add more tests with clock trees and inference of ancestral states -- Fredrik
 - Check Igr prior -- Fredrik
 - Check Brownian motion prior -- Fredrik
 - Correct brithdeath prior -- Fredrik
 - Update SetLikeFunctions() to incorparate SSE code -- Fredrik & Maxim
 - Fix codon model conflict with ParsSPR moves -- Fredrik
 - Introduce nst=mixed -- Fredrik
 - Test BEST code in mpi -- Fredrik
 - Realloc cmdline when reading exe files with long lines -- Maxim
 - Check that tree mix-up problem when check-pointing in MPI is gone -- Fredrik
 - Svn version number -- Maxim
 - Run tests on clock and relaxed clock trees, produce diagrams for publication -- Maxim
 - Make the starting trees=parsimony to work -- Maxim
 - Update CondLikeUp_XXX, PrintAncStates_XXX and  PrintSiteRates_XXX -- Maxim
 - Revert to non-SSE non-Beagle versions when models or setting do not allow SSE or Beagle -- Maxim
 - Make  install packages for Windows -- Maxim
 - Add a command ss that does step sampling (thermodynamic integration). -- Maxim
 - Add support for more sophisticated constraints. -- Maxim
 - Run test against Beast (dating paper) -- Maxim
 - Run regular model test files using beagleCPU, beagleGPU, SSE and regular likelihood calculators -- Maxim (some issues with BeagleGPU)


MAXIM

 1 Make executables and install packages for Mac (convenient for repeated production of installers)
 2 Add a command readfasta <filename> that reads a FASTA file of sequences into a matrix.
 3 Make it possible to read a Nexus matrix with single-quoted taxon names.
 4 Configure file for MrBayes and Beagle (best way of distributing mrbayes with beagle) also NDEBUG

 - Make a script or find a tool which converts Latex to html 
 - Beagle GPU issues
 - Run test againgst Phycas (standard nonclock tree with some complex model, see instructions at molecularevolution.org)

 - Make SSE and Beagle versions for reported anc states
 - Add starting trees=neighbor joining (nj)
 - Look at FAST_LOG for SSE
 - Implement a shortcut that skips fully ambiguous parts of the tree (?)
 - Implement recovery from checkpoints for stepping stone (stepping stone data has to be stored to .ckp file first)
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 - Profiling
 - Alternative ways of scaling?


FREDRIK
 - Email to mrbayes users email list, evoldir, systematikforeningen
 - Modify and finish manual
 - Rename gibbsGamma to samplerates, restructure as ordinary parameter
 - Rename relaxed clock models: igr to igr, bm to tk02
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 - Introduce cppi, mixedcpp, and mixedbr models (?)
 - Introduce catrate model
 - Fill in identity or stationary matrix in TiProbs_Std() if brl is extreme 


CHI
 - Extend coalescent prior and birth-death prior to serially sampled trees
 - Introduce fossils on ancestral branches with several sampling strategies
 - rjMCMC between relaxed clock models (TK02 and IGR)
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NOT ASSIGNED
 - Make PrunePolyTree() function to handle properly relaxed model parameters.
 - Improve parsSets implementation to be safer and more memory-efficient
 - Update web site, Wiki manual, online html help
 - Test parsimony models
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 - Introduce sampleomega

