@string{AHG         = "Annals of Human Genetics"}
@string{AJHG        = "American Journal of Human Genetics"}
@string{ARB         = "Annual Review of Biochemistry"}
@string{ARCB        = "Annual Review of Cell Biology"}
@string{BMCBI       = "BMC Bioinformatics"}
@string{BI          = "Bioinformatics"}
@string{BIOGEN      = "Biochemical Genetics"}
@string{BJLS        = "Biological Journal of the Linnean Society"}
@string{BMB         = "Bulletin of Mathematical Biology"}
@string{CABIOS      = "Computer Applications in the Biosciences"}
@string{CELL        = "Cell"}
@string{CACM        = "Communications of the ACM"}
@string{COCB        = "Current Opinion in Cell Biology"}
@string{COGD        = "Current Opinion in Genetics and Development"}
@string{COSB        = "Current Opinion in Structural Biology"}
@string{CSHSQB      = "Cold Spring Harbor Symposia Quantitative Biology"}
@string{ComputChem  = "Computers and Chemistry"}
@string{EMBO        = "EMBO Journal"}
@string{EVO         = "Evolution"}
@string{GEN         = "Genetics"}
@string{GB          = "Genome Biology"}
@string{GR          = "Genome Research"}
@string{JBSD        = "Journal of Biomolecular Structure and Dynamics"}
@string{JComputBiol = "Journal of Computational Biology"}
@string{JCB         = JComputBiol}
@string{JMB         = "Journal of Molecular Biology"}
@string{JME         = "Journal of Molecular Evolution"}
@string{JRSS        = "Journal of the Royal Statistical Society, B"}
@string{JTB         = "Journal of Theoretical Biology"}
@string{MBE         = "Molecular Biology and Evolution"}
@string{MBIO        = "Mathematical Biosciences"}
@string{MCB         = "Molecular Cell Biology"}
@string{ME          = "Methods in Enzymology"}
@string{MPE         = "Molecular Phylogenetics and Evolution"}
@string{NAR         = "Nucleic Acids Research"}
@string{NC          = "Neural Computation"}
@string{NNB         = "Nature New Biology"}
@string{NG          = "Nature Genetics"}
@string{NB          = "Nature Biotechnology"}
@string{Nature      = "Nature"}
@string{PE          = "Protein Engineering"}
@string{PLOSCOMPBIO = "PLoS Computational Biology"}
@string{PNAS        = "Proceedings of the National Academy of Sciences of the USA"}
@string{PROT        = "Proteins"}
@string{PROTSCI     = "Protein Science"}
@string{SIAM        = "SIAM Journal of Applied Mathematics"}
@string{SYSB        = "Systematic Biology"}
@string{SZ          = "Systematic Zoology"}
@string{Science     = "Science"}
@string{S           = Science}
@string{TIBTECH     = "Trends in Biotechnology"}
@string{TIGS        = "Trends in Genetics"}
@string{UKSB        = "University of Kansas Scientific Bulletin"}


%*********************************************************************************
% A
%*********************************************************************************

@Article{adachi92,
  author    = {J. Adachi and M. Hasegawa},
  title     = {Amino acid substitution of proteins coded for in mitochondrial {DNA} during mammalian evolution},
  journal   = {Jpn. J. Genet.},
  year      = 1992,
  volume    = 67,
  pages     = {187--197}
}

@Article{adachi95,
  author    = {J. Adachi and M. Hasegawa},
  title     = {Phylogeny of whales: {D}ependence of the inference on species sampling},
  journal   = {Molecular Biology and Evolution},
  year      = 1995,
  volume    = 12,
  pages     = {177--179}
}

@Article{adachi96,
  author    = {J. Adachi and M. Hasegawa},
  title     = {{MOLPHY Version 2.3}: {P}rograms for molecular phylogenetics based on maximum likelihood},
  journal   = {Computer Science Monographs},
  year      = 1996,
  volume    = 28,
  pages     = {1--150}
}

@Article{adachi00,
  author    = {J. Adachi and P. Waddell and W. Martin and M. Hasegawa},
  title     = {Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast {DNA}},
  journal   = {Journal of Molecular Evolution},
  year      = 2000,
  volume    = 50,
  pages     = {348--358}
}

@Article{adey94,
  author    = {N. B. Adey and T. O. Tollefsbol and A. B. Sparks and M. H. Edgell and C. A. Hutchison III},
  title     = {Molecular resurrecton of an extinct ancestral promoter for mouse {L1}},
  journal   = {Proceedings of the National Academy of Sciences, USA},
  year      = 1994,
  volume    = 91,
  pages     = {1569--1573}
}

@Article{adkins91,
  author    = {R. M. Adkins and R. L. Honeycutt},
  title     = {Molecular phylogeny of the superorder {A}rchonta},
  journal   = {Proceedings of the National Academy of Sciences, USA},
  year      = 1991,
  volume    = 88,
  pages     = {10317--10321}
}

@InProceedings{aldous85,
  author    = {D. Aldous},
  booktitle = {\'Ecole d'\'Et\'e de Probabilit\'es de Saint-Flour XIII-1983},
  title     = {Exchangeability ad related topics},
  publisher = {Springer, Berlin},
  year      = 1985,
  pages     = {1--198}
}

@Article{alfaro06,
  author    = {M. E. Alfaro and J. P. Huelsenbeck},
  title     = {Comparative performance of {B}ayesian and {AIC}-based measures of phylogenetic model uncertainty},
  journal   = {Systematic Biology},
  year      = 2006,
  volume    = 55,
  pages     = {89--96}
}

@Article{altekar04,
  author    = {G. Altekar and S. Dwarkadas and J. P. Huelsenbeck and F. Ronquist},
  title     = {Parallel {M}etropolis coupled {M}arkov chain {M}onte {C}arlo for {B}ayesian phylogenetic inference},
  journal   = {Bioinformatics},
  year      = 2004,
  volume    = 20,
  pages     = {407--415}
}

@Article{allman08a,
  author    = {E. S. Allman and C. An\'e and J. A. Rhodes},
  title     = {Identifiability of a {M}arkovian model of molecular evolution with gamma-distributed rates},
  journal   = {Advances in Applied Probability},
  year      = 2008,
  volume    = 40,
  pages     = {228--249}
}

@Article{allman08b,
  author    = {E. S. Allman and J. A. Rhodes},
  title     = {Identifying evolutionary trees and substitution parameters for the general {M}arkov model with invariable sites},
  journal   = {Mathematical Biosciences},
  year      = 2008,
  volume    = 211,
  pages     = {18--33}
}

@Article{allman09,
  author    = {E. S. Allman and J. A. Rhodes},
  title     = {The identifiability of covarion models in phylogenetics},
  journal   = {IEEE/ACM Transactions in Computational Biology and Bioinformatics},
  year      = 2009,
  volume    = 6,
  pages     = {76--88}
}

@Article{ammerman92,
  author    = {L. K. Ammerman and D. M. Hillis},
  title     = {A molecular test of bat relationships: {M}onophyly or diphyly?},
  journal   = {Systematic Biology},
  year      = 1992,
  volume    = 41,
  pages     = {222--232}
}

@Article{ane07,
  author    = {C. An\'e and B. Larget and D. A. Baum and S. D. Smith and A. Rokas},
  title     = {Bayesian estimation of concordance among gene trees},
  journal   = {Molecular Biology and Evolution},
  year      = 2007,
  volume    = 24,
  pages     = {412--426}
}

@Article{andolfatto05,
  author    = {P. Andolfatto},
  title     = {Adaptive evolution of non-coding {DNA} in {D}rosophila},
  journal   = {Nature},
  year      = 2005,
  volume    = 437,
  pages     = {1149--1153}
}

@Article{antoniak74,
  author    = {C. E. Antoniak},
  title     = {Mixtures of {D}irichlet processes with applications to non-parametric problems},
  journal   = {Annals of Statistics},
  year      = 1974,
  volume    = 2,
  pages     = {1152--1174}
}

@Article{arora96,
  author    = {R. Arora and C. Priano and A. Jacobson and D. R. Mills},
  title     = {Cis-acting elements within an {RNA} coliphage genome: {F}old as you please, but fold you must!!},
  journal   = {Journal of Molecular Biology},
  year      = 1996,
  volume    = 258,
  pages     = {433--446}
}

@Unpublished{arvestad99,
  author    = {Lars Arvestad},
  title     = {Practical algorithms for optimal accuracy alignment},
  year      = 1999,
  note      = {In preparation}
}

@Article{asmussen92,
  author    = {S. Asmussen and P. W. Glynn and H. Thorisson},
  title     = {Stationary detection in the initial transient problem},
  journal   = {ACM Trans. Model. Comput. Simul.},
  year      = 1992,
  volume    = 2,
  pages     = {130--157}
}

%*********************************************************************************
% B
%*********************************************************************************

@Article{bailey92,
  author    = {W. J. Bailey and J. L. Slightom and M. Goodman},
  title     = {Rejection of the ``Flying Primate'' hypothesis by phylogenetic evidence from $\epsilon$-globin gene},
  journal   = {Science},
  year      = 1992,
  volume    = 256,
  pages     = {86--89}
}

@Article{bailly03,
  author    = {X. Bailly and R. Leroy and S. Carney and O. Collin and F. Zal and A. Toulmond and D. Jollivet},
  title     = {The loss of the hemoglobin {H2S}-binding function in annelids from sulfide-free habitats reveals molecular adaptation driven by {D}arwinian positive selection.},
  journal   = {Proceedings of the National Academy of Science, U. S. A.},
  year      = 2003,
  volume    = 100,
  pages     = {5885--5890}
}

@Article{baker91,
  author    = {R. J. Baker and R. L. Honeycutt and R. A. Van Den Bussche},
  title     = {Examination of the monophyly of bats: {R}estriction map of the ribosomal {DNA} cistron},
  journal   = {Bulletin of the American Museum of Natural History},
  year      = 1991,
  volume    = 206,
  pages     = {42--53}
}

@Article{barry87,
  author    = {D. Barry and J. A. Hartigan},
  title     = {Statistical analysis of hominoid molecular evolution},
  journal   = {Stat. Sci.},
  year      = 1987,
  volume    = 2,
  pages     = {191--210}
}

@InProceedings{baserga93,
  author    = {S. J. Baserga and J. A. Steitz},
  editor    = {R. F. Gesteland and J. F. Atkins},
  booktitle = {The {RNA} {W}orld},
  title     = {The diverse world of small ribonucleoproteins},
  publisher = {Cold Spring Harbor Press},
  year      = 1993,
  pages     = {359--381}
}

@Article{bastolla01,
  author    = {U. Bastolla and J. Farwer and E. W. Knapp and M. Vendruscolo},
  title     = {How to guarantee optimal stability for most representative structures in the protein data bank},
  journal   = {Proteins},
  year      = 2001,
  volume    = 44,
  pages     = {79--96}
}

@Book{bayes36,
  author    = {T. Bayes},
  title     = {An {I}ntroduction to the {D}octrine of {F}luxions, and a {D}efence of the {M}athematicians against the objections of the {A}uthor of the {A}nalyst},
  publisher = {unknown publisher},
  year      = 1736,
  address   = {unknown address}
}

@Article{bayes63,
  author    = {T. Bayes},
  title     = {An essay towrds solving a problem in the doctrine of chances},
  journal   = {Philosophical Transactions of the Royal Society of London},
  year      = 1763,
  volume    = 53,
  pages     = {370--418}
}

@Article{beatty79,
  author    = {J. Beatty and W. L. Fink},
  title     = {Review of `{S}implicity' by {E}. {S}ober},
  journal   = {Systematic Zoology},
  year      = 1979,
  volume    = 28,
  pages     = {643--651}
}

@Article{beerli99,
  author    = {P. Beerli and J. Felsenstein},
  title     = {Maximum likelihood estimation of migration rates and effective population umbers in two populations using a coalescent approach},
  journal   = {Genetics},
  year      = 1999,
  volume    = 152,
  pages     = {763--773}
}

@Article{beiko05,
  author    = {R. G. Beiko and T. J. Harlow and M. A. Ragan},
  title     = {Highways of gene sharing in prokaryotes},
  journal   = {Proceedings of the National Academy of Science, U.S.A.},
  year      = 2005,
  volume    = 102,
  pages     = {14332--14337}
}

@Article{bell34,
  author    = {E. T. Bell},
  title     = {Exponential numbers},
  journal   = {American Mathematics Monthly},
  year      = 1934,
  volume    = 41,
  pages     = {411--419}
}

@Article{berger99,
  author    = {J. O. Berger and B. Liseo and R. L. Wolpert},
  title     = {Integrated likelihood methods for eliminating nuisance parameters},
  journal   = {Statistical Science},
  year      = 1999,
  volume    = 14,
  pages     = {1--28}
}

@Article{birney07,
  author    = {{ENCODE} project consortium},
  title     = {{I}dentification and analysis of functional elements in 1\% of the human genome by the {E}{N}{C}{O}{D}{E} pilot project},
  journal   = Nature,
  year      = 2007,
  volume    = 7146,
  pages     = {799--816}
}

@Article{bishop85,
  author    = {M. J. Bishop and A. E. Friday},
  title     = {Evolutionary trees form nucleic acid and protein sequences},
  journal   = {Proceedings of the Royal Society of London, B},
  year      = 1985,
  volume    = 226,
  pages     = {271--302}
}

@InProceedings{bishop87,
  author    = {M. J. Bishop and A. E. Friday},
  editor    = {C. Patterson},
  booktitle = {Molecules and {M}orphology in {E}volution: {C}onflict or {C}ompromise?},
  title     = {Tetrapod relationships: {T}he molecular evidence},
  publisher = {Cambridge University Press},
  year      = 1987,
  pages     = {123--140}
}

@Article{blake92,
  author    = {R. D. Blake and S. T. Hess and J. Nicholson-Tuell},
  title     = {EvoThe influence of nearest neighbors on the rate and pattern of spontaneous point mutations},
  journal   = {JME},
  year      = 1992,
  volume    = 34,
  pages     = {189--200}
}

@InProceddings{bollback04,
  author    = {J. Bollback},
  editor    = {R. Nielsen},
  booktitle = {Statistical Methods in Molecular Evolution},
  title     = {Predictive distributions and posterior mappings},
  publisher = {Springer-Verlag},
  year      = 2004
}

@Article{bollback01,
  author    = {J. Bollback and J. P. Huelsenbeck},
  title     = {Phylogenetic relationships, genome evolution, and host specificity of single-stranded {RNA} bacteriophage ({F}amily {L}eviviridae)},
  journal   = {Journal of Molecular Evolution},
  year      = 2001,
  volume    = 52,
  pages     = {117--128}
}

@Phdthesis{bourque78,
  author    = {M. Bourque},
  title     = {Arbres de Steiner et reseaux dont varie l'emplagement de certains sommets},
  school    = {University of Montreal},
  year      = 1978,
}

@Article{brandley05,
  author    = {M. C. Brandley and A. Schmitz and T. W. Reeder},
  title     = {Partitioned {B}ayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards},
  journal   = {Systematic Biology},
  year      = 2005,
  volume    = 54,
  pages     = {373--390}
}

@Article{brandley08,
  author    = {M. C. Brandley and J. P. Huelsenbeck and J. J. Wiens},
  title     = {Rates and patterns in the evolution of snake-like body form in squamate reptiles: {E}vidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms},
  journal   = {Evolution},
  year      = 2008,
  volume    = 62,
  pages     = {2042--2064}
}

@Article{bradley07,
  Author    = "R. K. Bradley and I. Holmes",
  Title     = "{{T}ransducers: {A}n {E}merging {P}robabilistic {F}ramework for {M}odeling {I}ndels on {T}rees}",
  Journal   = BI,
  Year      = "2007",
  Month     = "Sep"
}

@Article{bray04,
  author    = {N. Bray and L. Pachter},
  title     = {{MAVID}: Constrained ancestral alignment of multiple sequences},
  journal   = GR,
  year      = 2004,
  volume    = 14,
  pages     = {693--699}
}

@Article{brochier02,
  author    = {C. Brochier and H. Philippe},
  title     = {Phylogeny: {A} non-hyperthermophilic ancestor for {B}acteria},
  journal   = {Nature},
  year      = 2002,
  volume    = 417,
  pages     = {244}
}

@Article{brower00,
  author    = {A. V. Z. Brower},
  title     = {Phylogenetic relationshiops among the {N}ymphalidae ({L}epidoptera) inferred from partial sequences of the wingless gene},
  journal   = {Proceedings of the Royal Society London, Series B},
  year      = 2000,
  volume    = 267,
  pages     = {1201--1211}
}

@Article{brown82,
  author    = {W. M. Brown and E. M. Prager and A. Wang and A. C. Wilson},
  title     = {Mitochondrial {DNA} sequences of primates, tempo and mode of evolution},
  journal   = {Journal of Molecular Evolution},
  year      = 1982,
  volume    = 18,
  pages     = {225--239}
}

@Article{brown93,
  author    = {M. Brown and R. Hughey and A. Krogh and I. S. Mian and K. Sj{\"o}lander and D. Haussler},
  title     = "Using {D}irichlet Mixture Priors to Derive Hidden {M}arkov Models for Protein Families",
  journal   = {Proc. of First Int. Conf. on Intelligent Systems for Molecular Biology},
  year      = 1993,
  pages     = "47--55",
}

@Article{brown07,
  author    = {J. M. Brown and A. R. Lemmon},
  title     = {The importance of data partitioning and the utility of {B}ayes factors in {B}ayesian phylogenetics},
  journal   = {Systematic Biology},
  year      = 2007,
  volume    = 56,
  pages     = {643--655}
}

@Article{bryant00,
  author    = {D. Bryant and J. Tsang and P. Kearney and M. Li},
  title     = {Computing the quartet distance between evolutionary trees},
  journal   = {Proceedings of the ACM-SIAM Symposium on Discrete Algorithms},
  year      = 2000
}

@Article{bulmer86,
  author    = {M. Bulmer},
  title     = {Neighboring base effects on substitution rates in pseudo genes},
  journal   = {MBE},
  year      = 1986,
  volume    = 3,
  pages     = {322--329}
}

@Article{bull93,
  author    = {J. J. Bull and J. P. Huelsenbeck and C. W. Cunningham and D. L. Swofford and P. J. Waddell},
  title     = {Partitioning and combining data in phylogenetic analysis},
  journal   = {Systematic Biology},
  year      = 1993,
  volume    = 42,
  pages     = {384--397}
}

%*********************************************************************************
% C
%*********************************************************************************

@Article{cameron07,
  author    = {S. Cameron and H. M. Hines and P. H. Williams},
  title     = {A comprehensive phylogeny of bumble bees ({B}ombus)},
  journal   = {Biological journal of the Linnean Society},
  year      = 2007,
  volume    = 91,
  pages     = {161--188}
}

@Article{camin65,
  author    = {J. H. Camin and R. R. Sokal},
  title     = {A method for deducing branching sequences in a phylogeny},
  journal   = {Evolution},
  year      = 1965,
  volume    = 19,
  pages     = {311--326}
}

@Article{cann87,
  author    = {R. L. Cann and M. Stoneking and A. C. Wilson},
  title     = {Mitochondrial {DNA} and human evolution},
  journal   = {Nature},
  year      = 1987,
  volume    = 325,
  pages     = {31--36}
}

@Article{cao98,
  author    = {Y. Cao and A. Janke and P. J. Waddell and M. Westerman and O. Takenaka and S. Murata and N. Okada and S. P\"a\"abo and M. Hasegawa},
  title     = {Conflict amongst individual mitochondrial proteins in resolving the phylogeny of eutherian orders},
  journal   = {Journal of Molecular Evoluton},
  year      = 1998,
  volume    = 47,
  pages     = {307--322}
}

@Book{carlin00,
  author    = {B. P. Carlin and T. A. Louis},
  title     = {Bayes and Empirical {B}ayes Methods for Data Analysis},
  publisher = {Chapman and Hall/CRC},
  year      = 2000,
  address   = {Boca Raton},
  edition   = {second}
}

@Article{cavalli-sforza67,
  author    = {L. L. Cavalli-Sforza and A. W. F. Edwards},
  title     = {Phylogenetic analysis. {M}odels and estimation procedures},
  journal   = {American Journal of Human Genetics},
  year      = 1967,
  volume    = 19,
  pages     = {233--257}
}

@Book{cavalli-sforza94,
  author    = {L. L. Cavalli-Sforza and P. Menozzi and A. Piazza},
  title     = {History and {G}eography of {H}uman {G}enes},
  publisher = {Princeton University Press},
  year      = 1994,
  address   = {Princeton, New Jersey}
}

@Article{cavelaars00,
  author    = {A. E. J. M. Cavelaars and  A. E. Kunst and  J. J. M. Geurts and R. Crialesi and  L. Gr\"otvedt and  U. Helmert and  E. Lahelma and  O. Lundberg and  A. Mielck and  N. Kr. Rasmussen and E. Regidor and T. Spuhler and J. P. Mackenbach},
  title     = {Persistent variations in average height between countries and between socio-economic groups: {A}n overview of 10 European countries},
  journal   = {Annals of Human Biology},
  year      = 2000,
  volume    = 27,
  pages     = {407--421}
}

@Article{cavender78,
  author    = {J. A. Cavender},
  title     = {Taxonomy with confidence},
  journal   = {Mathematical Biosciences},
  year      = 1978,
  volume    = 40,
  pages     = {301--316}
}

@Article{cavender87,
  author    = {J. A. Cavender and J. Felsenstein},
  title     = {Invariants of phylogenies in a simple case with discrete states},
  journal   = {Journal of Classification},
  year      = 1987,
  volume    = 4,
  pages     = {57--71}
}

@Article{cech86,
  author    = {T. R. Cech and B. L. Bass},
  title     = {Biological catalysis by {RNA}},
  journal   = {Annual Review of Biochemistry},
  year      = 1986,
  volume    = 55,
  pages     = {599--629}
}

@Article{chandrasekharan96,
  author    = {U. M. Chandrasekharan and S. Sanker and M. J. Glynias and S. S. Karnik and A. Husain},
  title     = {Angiotensin II-forming activity in a reconstructed ancestral chymase},
  journal   = {Science},
  year      = 1996,
  volume    = 271,
  pages     = {1483--1489}
}

@Article{chang00,
  author    = {B. S. W. Chang and M. J. Donoghue},
  title     = {Recreating ancestral proteins},
  journal   = {Trends in Ecology and Evolution},
  year      = 2000,
  volume    = 15,
  pages     = {109--114}
}

@Article{chang02,
  author    = {B. S. W. Chang and K. J\"onsson and M. A. Kazmi and M. J. Donoghue and T. P. Sakmar},
  title     = {Recreating a functional ancestral {A}rchosaur visual pigment},
  journal   = {Molecular Biology and Evolution},
  year      = 2002,
  volume    = 19,
  pages     = {502--505}
}

@Phdthesis{charleston94,
  author    = {M. A. Charleston},
  title     = {Factors affecting the performance of phylogenetic methods},
  school    = {Massey University},
  year      = 1994,
}

@Article{charleston95,
  author    = {M. A. Charleston},
  title     = {Toward a characterization of landscapes of combinatorial optimization problems, with special attention to the phylogeny problem},
  journal   = {Journal of Computational Biology},
  year      = 1995,
  volume    = 2,
  pages     = {439--450}
}

@Article{chase93,
  author    = {M. W. Chase and D. E. Soltis and R. G. Olmstead and D. Morgan and D. H. Les and B. D.  Mishler and M. R. Duvall and R. A. Price and H. G. Hills and Y. Qiu and K. A. Kron and  J. H. Rettig and E. Conti and J. D. Palmer and J. R. Manhart and K. J. Sytsma and  H. J. Michaels and W. J. Kress and K. G. Karol and W. D. Clark and M. Hedren and B. S.  Gaut and R. K. Jansen and K. Kim and C. F. Wimpee and J. F. Smith and G. R. Furnier and S. H. Strauss and Q. Xiang and G. M. Plunkett and P. S. Soltis and S. M. Swensen and  S. E. Williams and P. A. Gadek and C. J. Quinn and L. E. Eguiarte and E. Golenberg and G. H. Learn and S. W. Graham and S. C. H. Barrett and S. Dayanandan and V. A. Albert},
  title     = {Phylogenetics of seed plants: {A}n  analysis of nucleotide sequences from the plastid gene rbcL},
  journal   = {Annals Missouri Botanical Garden},
  year      = 1993,
  volume    = 80,
  pages     = {528--580}
}

@Article{chothia86,
  author    = {C. Chothia and A. M. Lesk},
  title     = {The relation between the divergence of sequence and structure in proteins},
  journal   = {EMBO J},
  year      = 1986,
  volume    = 5,
  pages     = {823--826}
}

@Article{clark03,
  author    = {A. G. Clark and S. Glanowski and R. Nielsen and P. D. Thomas and A. Kejariwal and M. A. Todd and D. M. Tanenbaum and D. Civello and F. Lu and B. Murphy and S. Ferriera and G. Wang, X. Zheng and T. J. White and J. J. Sninsky and M. D. Adams and M. Cargill},
  title     = {Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios},
  journal   = {Science},
  year      = 2003,
  volume    = 302,
  pages     = {1960--1963}
}

@Article{cliften01,
  author    = {P. Cliften and L. W. Hillier and L. Fulton and T. Graves and T. Miner W. R. Gish and R. H. Waterston and M. Johnston},
  title     = {Surveying {\it {S}accharomyces} genomes to identify functional elements by comparative {DNA} sequence analysis},
  journal   = {Genome Research},
  year      = 2001,
  volume    = 11,
  pages     = {1175--1186}
}

@Article{cliften03,
  author    = {P. Cliften and P. Sudarsanam and A. Desikan and L. Fulton and B. Fulton and J. Majors and R. Waterson and B. A. Cohen and M. Johnston},
  title     = {Finding functional features in {\it {S}accharomyces} genomes by phylogenetic footprinting},
  journal   = {Science},
  year      = 2003,
  volume    = 301,
  pages     = {71--76}
}

@Article{colless82,
  author    = {D. H. Colless},
  title     = {Review of Phylogenetics: The theory and practice of phylogenetic systematics II},
  journal   = {Systematic Zoology},
  year      = 1982,
  volume    = 31,
  pages     = {100--104}
}

@Article{cornish85,
  author    = {A. Cornish-Bowden},
  title     = {Nomenclature for incompletely specified bases in nucleic acid sequences: {R}ecommendations 1984},
  journal   = {Nucleic Acids Research},
  year      = 1985,
  volume    = 13,
  pages     = {3021--3030}
}

@Book{coyne04,
  author    = {J. A. Coyne and H. A. Orr},
  title     = {Speciation},
  publisher = {Sinauer Associates, Inc.},
  year      = 2004,
  address   = {Sunderland, Massachusetts}
}

@Book{crowson81,
  author    = {R. A. Crowson},
  title     = {The Biology of {C}oleoptera},
  publisher = {Academic Press},
  year      = 1981,
  address   = {London}
}

@Article{cunningham92,
  author    = {C. W. Cunningham and N. W. Blackstone and L. W. Buss},
  title     = {Evolution of king crabs from hermit crab ancestors},
  journal   = {Nature},
  year      = 1992,
  volume    = 335,
  pages     = {539--542}
}

@Article{cummings95,
  author    = {M. P. Cummings and S. P. Otto and J. Wakeley},
  title     = {Sampling properties of DNA sequence data in phylogenetic analysis},
  journal   = {Molecular Biology and Evolution},
  year      = 1995,
  volume    = 12,
  pages     = {814--822}
}

%*********************************************************************************
% D
%*********************************************************************************

@Book{darwin59,
  author    = {C. Darwin},
  title     = {On the {O}rigin of {S}pecies},
  publisher = {J. Murray},
  year      = 1859,
  address   = {London}
}

@InProceedings{dayhoff78,
  author    = {M. O. Dayhoff and R. M. Schwartz and B. C. Orcutt},
  title     = {A model of evolutionary change in proteins},
  booktitle = {Atlas of protein sequence and structure, Volume 5, Supplement 3},
  publisher = {National Biomedical Research Foundation},
  year      = 1978,
  pages     = {345--352}
}

@Article{definetti37,
  author    = {B. de Finetti},
  title     = {le pr\'evision: ses lois logiques, ses sources subjectives},
  journal   = {Ann. Inst. Poincare},
  year      = 1937,
  volume    = 7,
  pages     = {1--68}
}

@Article{dequeiroz90,
  author    = {K. de Queiroz and J. Gauthier},
  title     = {Phylogeny as a central principle in taxonomy: {P}hylogenetic definitions of taxon names},
  journal   = {Systematic Zoology},
  year      = 1990,
  volume    = 39,
  pages     = {307--322}
}

@Article{dequeiroz92,
  author    = {K. de Queiroz and J. Gauthier},
  title     = {Phylogenetic taxonomy},
  journal   = {Annual Review of Ecology and Systematics},
  year      = 1992,
  volume    = 23,
  pages     = {449--480}
}

@Article{dequeiroz94,
  author    = {K. de Queiroz and J. Gauthier},
  title     = {Toward a phylogenetic system of biological nomenclature},
  journal   = {Trends in Ecology and Evolution},
  year      = 1994,
  volume    = 9,
  pages     = {27--31}
}

@Article{diaconis07,
  author    = {P. Diaconis and S. Holmes and R. Montgomery},
  title     = {Dynamical bias in the coin toss},
  journal   = {SIAM Review},
  year      = 2007,
  volume    = 49,
  pages     = {211--235}
}

@Article{dickey71,
  author    = {J. Dickey},
  title     = {The weighted likelihood ratio, linear hypotheses on normal location parameters},
  journal   = {The Annals of Statistics},
  year      = 1971,
  volume    = 42,
  pages     = {204--223}
}

@Article{dimmic02,
  author    = {M. W. Dimmic and J. S. Rest and D. P. Mindell and D. Goldstein},
  title     = {{RA}rt{REV}: {A}n amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny},
  journal   = {Journal of Molecular Evolution},
  year      = 2002,
  volume    = 55,
  pages     = {65--73}
}

@InProceedings{dimmic04,
  author    = {M. Dimic},
  editor    = {R. Nielsen},
  booktitle = {Statistical Methods in Molecular Evolution},
  title     = {Models of protein evolution},
  publisher = {Springer-Verlag},
  year      = 2004
}

@Article{do05,
  author    = {C. B. Do and M. S. P. Mahabhashyam and M. Brudno and S. Batzoglou},
  title     = {{PROBCONS}: {P}robabilistic consistency-based multiple sequence alignment},
  journal   = {Genome Research},
  year      = 2005,
  volume    = 15,
  pages     = {330--340}
}

@InProceedings{dongarra84,
  author    = {J. J. Dongarra and G. W. Stewart},
  editor    = {W. R. Cowell},
  booktitle = {Sources and Development of Mathematical Software},
  title     = {{PROBCONS}: {P}robabilistic consistency-based multiple sequence alignment},
  publisher = {Prentice-Hall},
  pages     = {20--48},
  year      = 1984
}

@Article{dongarra75,
  author    = {J. J. Dongarra and B. S. Garbow},
  title     = {Path chart and documentation for the {EISPACK} package of matrix eigensystem routines},
  journal   = {Argonne National Laboratory Technical Memorandum},
  year      = 1975,
  pages     = {ANL-AMD-TM-250}
}

@InProceedings{durrett04,
  author    = {R. Durrett},
  editor    = {R. Nielsen},
  booktitle = {Statistical Methods in Molecular Evolution},
  title     = {Evolution by genome rearrangement},
  publisher = {Springer-Verlag},
  year      = 2004
}

@Article{donoghue92,
  author    = {M. J. Donoghue and J. W. Kadereit},
  title     = {Walter Zimmermann and the growth of phylogenetic theory},
  journal   = {Systematic Biology},
  year      = 1992,
  volume    = 41,
  pages     = {74--85}
}

@Book{drucker59,
  author    = {P. Drucker},
  title     = {Landmarks of {T}omorrow},
  publisher = {Harper},
  year      = 1959,
  address   = {New York}
}

@Article{drummond06,
  author    = {A. J. Drummond and S. Y. Ho and M. J. Phillips and A. Rambaut},
  title     = {Relaxed phylogenetics and dating with confidence},
  journal   = {PLoS Biology},
  year      = 2006,
  volume    = 4,
  pages     = {e88}
}

@Misc{drummond07,
  author       = {A. Drummond and A. Rambaut},
  title        = {{BEAST} v1.4},
  howpublished = {http://beast.bio.ed.ac.uk},
  year         = 2007
}

@Article{drummond10,
  author    = {A. J. Drummond and M. A. Suchard},
  title     = {Bayesian random local clocks, or one rate to rule them all},
  journal   = {BMC Biology},
  year      = 2010,
  volume    = 8,
  pages     = {114}
}

@Book{durbin98,
  author    = {R. Durbin and S. Eddy and A. Krogh and G. Mitchison},
  title     = {Biological {S}equence {A}nalysis},
  publisher = {Cambridge University Press},
  year      = 1998,
  address   = {Cambridge}
}

%*********************************************************************************
% E
%*********************************************************************************

@Article{eddy95,
  author    = "S. R. Eddy and G. J. Mitchison and R. Durbin",
  title     = "Maximum Discrimination Hidden {M}arkov Models of Sequence Consensus",
  journal   = JComputBiol,
  year      = 1995,
  volume    = 2,
  pages     = "9--23"
}

@Article{edgar04,
  author    = {R. C. Edgar},
  title     = {{MUSCLE}: {M}ultiple sequence alignment with high accuracy and high throughput},
  journal   = {Nucleic Acids Research},
  year      = 2004,
  volume    = 32,
  pages     = {1792--1797}
}

@Article{edwards66,
  author    = {A. W. F. Edwards},
  title     = {Studying human evolution by computer},
  journal   = {New Scientist},
  year      = 1966,
  volume    = 30,
  pages     = {438--440}
}

@Article{edwards70,
  author    = {A. W. F. Edwards},
  title     = {Estimation of the branch points of a branching diffusion process},
  journal   = {Journal of the Royal Statistical Society B},
  year      = 1970,
  volume    = 32,
  pages     = {155--174}
}

@Book{edwards72,
  author    = {A. W. F. Edwards},
  title     = {Likelihood},
  publisher = {Cambridge University Press},
  year      = 1972,
  address   = {Cambridge}
}

@Article{edwards96,
  author    = {A. W. F. Edwards},
  title     = {The origin and early development of the method of minimum evolution for the reconstruction of phylogenetic trees},
  journal   = {Systematic Biology},
  year      = 1996,
  volume    = 45,
  pages     = {79--91}
}

@Article{edwards63,
  author    = {A. W. F. Edwards and L. L. Cavalli-Sforza},
  title     = {The reconstruction of evolution (Abstract)},
  journal   = {Annals of Human Genetics},
  year      = 1963,
  volume    = 27,
  pages     = {104--105}
}

@InProceedings{edwards64,
  author    = {A. W. F. Edwards and L. L. Cavalli-Sforza},
  editor    = {J. McNeill},
  booktitle = {Phenetic and {P}hylogenetic {C}lassification},
  title     = {Reconstruction of evolutionary trees},
  publisher = {Systematics Association Publication},
  year      = 1964
}

@article{edwards07,
author = {Scott V Edwards and Liang Liu and Dennis K Pearl}, 
title = {{High-resolution species trees without concatenation}},
journal = {Proc. Natl Acad. Sci. USA},
year = {2007},
volume = {104},
number = {14},
pages = {5936--41}
}

@Article{efron96,
  author    = {B. Efron and E. Halloran and S. Holmes},
  title     = {Bootstrap confidence levels for phylogenetic trees},
  journal   = {Proceedings of the National Academy of Science, USA},
  year      = 1996,
  volume    = 93,
  pages     = {13429--13434}
}

@Book{eldredge80,
  author    = {N. Eldredge and J. Cracraft},
  title     = {Phylogenetic {P}atterns and the {E}volutionary {P}rocess},
  publisher = {Columbia University Press},
  year      = 1980,
  address   = {New York}
}

@Article{elston71,
  author    = {R. C. Elston and J. Stewart},
  title     = {A general model for the genetic analysis of pedigree data},
  journal   = {Human Heredity},
  year      = 1971,
  volume    = 21,
  number    = 6,
  pages     = {523--542}
}

@Article{ehrlich90,
  author    = {M. Ehrlich and X. Y. Zhang and N. M. Inamdar},
  title     = {Spontaneous deamination of cytosine and 5-methylcytosine residues in {DNA} and replacement of 5-methylcytosine residues with cytosine residues},
  journal   = {Mutat. Res.},
  year      = 1990,
  volume    = 238,
  pages     = {277--286}
}

@InProceedings{ewens98,
  author    = {W. J. Ewens and S. Tavar\'e},
  editor    = {S. Kotz and C. B. Read and D. L. Banks},
  booktitle = {Encyclopedia of Statistical Science},
  title     = {The {E}wens sampling formula},
  publisher = {Wiley, New York},
  year      = 1998
}

%*********************************************************************************
% F
%*********************************************************************************

@Article{farris70,
  author    = {J. S. Farris},
  title     = {Methods for computing Wagner trees},
  journal   = {Systematic Zoology},
  year      = 1970,
  volume    = 19,
  pages     = {83--92}
}

@Article{farris73,
  author    = {J. S. Farris},
  title     = {A probability model for inferring evolutionary trees},
  journal   = {Systematic Zoology},
  year      = 1973,
  volume    = 22,
  pages     = {250--256}
}

@InProceedings{farris83,
  author    = {J. S. Farris},
  editor    = {N. I. Platnick and V. A. Funk},
  booktitle = {Advances in {C}ladistics, {V}olume 2},
  title     = {The logical basis of phylogenetic analysis},
  publisher = {Columbia University Press},
  year      = 1983,
  pages     = {7--36}
}

@Article{farris96,
  author    = {J. S. Farris and V. A. Albert and M. K\"allersj\"o and D. Lipscomb and A. G. Kluge},
  title     = {Parsimony jackknifing outperforms neighbor-joining},
  journal   = {Cladistics},
  year      = 1996,
  volume    = 12,
  pages     = {99--124}
}

@Article{farris08,
  author    = {J. S. Farris},
  title     = {Parsimony and explanatory power},
  journal   = {Cladistics},
  year      = 2008,
  volume    = 24,
  pages     = {825--847}
}

@Book{felsenstein04,
  author    = {J. Felsenstein},
  title     = {Inferring Phylogenies},
  publisher = {Sinauer Associates, Inc.},
  year      = 2004,
  address   = {Sunderland, Massachusetts}
}

@Phdthesis{felsenstein68,
  author    = {J. Felsenstein},
  title     = {Statistical inference and the estimation of phylogenies},
  school    = {University of Chicago},
  year      = 1968,
}

@Article{felsenstein73,
  author    = {J. Felsenstein},
  title     = {Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters},
  journal   = {Systematic Zoology},
  year      = 1973,
  volume    = 22,
  pages     = {240--249}
}

@Article{felsenstein78,
  author    = {J. Felsenstein},
  title     = {Cases in which parsimony and compatibility methods will be positively misleading},
  journal   = {Systematic Zoology},
  year      = 1978,
  volume    = 27,
  pages     = {401--411}
}

@Article{felsenstein81,
  author    = {J. Felsenstein},
  title     = {Evolutionary trees from {DNA} sequences:  {A} maximum likelihood approach},
  journal   = {Journal of Molecular Evolution},
  year      = 1981,
  volume    = 17,
  pages     = {368--376}
}

@Misc{felsenstein93,
  author       = {J. Felsenstein},
  title        = {{PHYLIP}: ({P}hylogeny {I}nference {P}ackage)},
  howpublished = {Distributed by author},
  year         = 1993
}

@Article{felsenstein85a,
  author    = {J. Felsenstein},
  title     = {Confidence limits on phylogenies: {A}n approach using the bootstrap},
  journal   = {Evolution},
  year      = 1985,
  volume    = 39,
  pages     = {783--791}
}

@Article{felsenstein85b,
  author    = {J. Felsenstein},
  title     = {Phylogenies and the comparative method},
  journal   = {The American Naturalist},
  year      = 1985,
  volume    = 125,
  pages     = {1--15}
}

@InProceedings{felsenstein88,
  author    = {J. Felsenstein},
  editor    = {D. L. Hawksworth},
  title     = {The detection of phylogeny},
  booktitle = {Prospects in {S}ystematics},
  publisher = {Systematics Association and Clarendon Press},
  year      = 1988,
  pages     = {112--127}
}

@Article{felsenstein96,
  author    = {J. Felsenstein and G. A. Churchill},
  title     = {A hidden {M}arkov model approach to variation among sites in rate of evolution},
  journal   = {Molecular Biology and Evolution},
  year      = 1996,
  volume    = 13,
  pages     = {93--104}
}

@Article{felsenstein01,
  author    = {J. Felsenstein},
  title     = {The troubled growth of statistical phylogenetics},
  journal   = {Systematic Biology},
  year      = 2001,
  volume    = 50,
  pages     = {465--467}
}

@Article{feng87,
  author    = {D. F. Feng and R. F. Doolittle},
  title     = {Progressive sequence alignment as a prerequisite to correct phylogenetic trees},
  journal   = {Journal of Molecular Evolution},
  year      = 1987,
  volume    = 25,
  pages     = {351--360}
}

@Article{ferguson73,
  author    = {T. S. Ferguson},
  title     = {A {B}ayesian analysis of some nonparametric problems},
  journal   = {Annals of Statistics},
  year      = 1973,
  volume    = 1,
  pages     = {209--230}
}

@Article{fisher12,
  author    = {R. A. Fisher},
  title     = {On an absolute criterion for fitting frquency curves},
  journal   = {Mess. Math.},
  year      = 1912,
  volume    = 41,
  pages     = {155--160}
}

@Article{fisher21,
  author    = {R. A. Fisher},
  title     = {On the `probable error' of a coefficient of correlation deduced from a  small sample},
  journal   = {Metron, I},
  year      = 1921,
  volume    = 4,
  pages     = {3--32}
}

@Article{fisher22,
  author    = {R. A. Fisher},
  title     = {On the mathematical foundations of theoretical statistics},
  journal   = {Philosophical Transactions of the Royal Society off London, A},
  year      = 1922,
  volume    = 222,
  pages     = {309--368}
}

@Book{fisher25,
  author    = {R. A. Fisher},
  title     = {Statistical {M}ethods for {R}esearch {W}orkers},
  publisher = {Oliver and Boyd},
  year      = 1925,
  address   = {Edinburgh}
}

@Article{fitch71,
  author    = {W. M. Fitch},
  title     = {Toward defining the course of evolution: Minimum change for a specific tree topology},
  journal   = {Systematic Zoology},
  year      = 1971,
  volume    = 20,
  pages     = {406--416}
}

@Article{fitch67,
  author    = {W. M. Fitch and E. Margoliash},
  title     = {Construction of phylogenetic trees},
  journal   = {Science},
  year      = 1967,
  volume    = 155,
  pages     = {279--284}
}

@Article{fitch97,
  author    = {W. M. Fitch and R. M. Bush and C. A. Bender and N. J. Cox},
  title     = {Long term trends in the evolution of {H(3)} {HA1} human influenza type {A}},
  journal   = {Proceedings of the National Academy of Science, U.S.A.},
  year      = 1997,
  volume    = 94,
  pages     = {7712--7718}
}

@Article{flores93,
  author    = {T. P. Flores and C. A. Orengo and D. S. Moss and J. M. Thornton},
  title     = {Comparison of conformational characteristics in structurally similar protein pairs},
  journal   = {Protein Science},
  year      = 1993,
  volume    = 2,
  pages     = {1811--1826}
}

@Article{forsberg03,
  author    = {R. Forsberg and F. B. Christiansen},
  title     = {A codon-based model of host-specific selection in parasites, with an application to the influenza virus},
  journal   = {Molecular Biology and Evolution},
  year      = 2003,
  volume    = 20,
  pages     = {1252--1259}
}

@Article{furnas84,
  author    = {G. W. Furnas},
  title     = {The generation of random, binary, unordered trees},
  journal   = {Journal of Classification},
  year      = 1984,
  volume    = 1,
  pages     = {187--233}
}

%*********************************************************************************
% G
%*********************************************************************************

@InProceedings{gaffney79,
  author    = {E. S. Gaffney},
  editor    = {J. Cracraft and N. Eldredge},
  title     = {An introduction to the logic of phylogeny  reconstruction},
  booktitle = {Phylogenetic {A}nalysis and {P}aleontology},
  publisher = {Columbia University Press},
  year      = 1979,
  pages     = {79--111}
}

@Article{gallager62,
  author    = {R. G. Gallager},
  title     = {Low-density parity-check codes},
  journal   = {IRE Trans. Inform. Theory},
  year      = 1962,
  volume    = 8,
  pages     = {21--28}
}

@Book{gallager63,
  author    = {R. G. Gallager},
  title     = {Low-density parity check codes},
  publisher = {MIT Press},
  year      = 1963,
  address   = {Cambridge, MA}
}

@Article{galtier01,
  author    = {N. Galtier},
  title     = {Maximum-likelihood phylogenetic analysis under a covarion-like model},
  journal   = {Molecular Biology and Evolution},
  year      = 2001,
  volume    = 18,
  pages     = {866--873}
}

@Article{galtier07,
  author    = {N. Galtier},
  title     = {A model of horizontal gene transfer and the bacterial phylogeny problem},
  journal   = {Systematic Biology},
  year      = 2007,
  volume    = 56,
  pages     = {663--642}
}

@Article{gao92,
  author    = {F. Gao and L. Yue and A. T. White and P. G. Pappas and J. Barchue and A. P. Hanson and B. M. Greene and P. M. Sharp and G. M. Shaw and B. H. Hahn BH},
  title     = {Human infection by genetically diverse {SIVSM}-related {HIV-2} in {W}est {A}frica},
  journal   = {Nature},
  year      = 1992,
  volume    = 358,
  pages     = {495--499}
}

@Article{gao99,
  author    = {F. Gao and E. Bailes and D. L. Robertson and Y. Chen and C. M. Rodenburg and S. F. Michael and L. B. Cummins and
               L. O. Arthur and M. Peeters and G. M. Shaw and P. M. Sharp and B. H. Hahn},
  title     = {Origin of {HIV-1} in the chimpanzee {\it {P}an troglodytes troglodytes}},
  journal   = {Nature},
  year      = 1999,
  volume    = 397,
  pages     = {436--441}
}

@Article{gaut95,
  author    = {B. A. Gaut and P. O. Lewis},
  title     = {Success of maximum likelihood in the four-taxon case},
  journal   = {Molecular Biology and Evolution},
  year      = 1995,
  volume    = 12,
  pages     = {152--162}
}

@Article{gauthier86,
  author    = {J. Gauthier},
  title     = {Saurischian monophyly and the origin of birds},
  journal   = {Mem. Cal. Acad. Sci.},
  year      = 1986,
  volume    = 8,
  pages     = {1--55}
}

@Article{gauthier88,
  author    = {J. Gauthier and A. G. Kluge and T. Rowe},
  title     = {Amniote phylogeny and the importance of fossils},
  journal   = {Cladistics},
  year      = 1988,
  volume    = 4,
  pages     = {105--209}
}

@Article{geman84,
  author    = {S. Geman and D. Geman},
  title     = {Stochastic relaxation, {G}ibbs distributions, and the {B}ayesian restoration of images},
  journal   = {{IEEE} Transactions on Patrtern Analysis and Machine Intelligence},
  year      = 1984,
  volume    = 6,
  pages     = {721--741}
}

@book{gamerman06,
    author = "Dani Gamerman and Hedibert F. Lopes",
    title = "Markov Chain {M}onte {C}arlo: Stochastic Simulation for {B}ayesian Inference",
    year = "2006",
    publisher = "Chapman and Hall",
    edition = "second"
}

@Article{gelman92,
  author    = {A. Gelman and D. B. Rubin},
  title     = {Inferences from iterative simulation using multiple sequences},
  journal   = {Statistical Science},
  year      = 1992,
  volume    = 7,
  pages     = {457--511}
}

@Book{gelman95,
  author    = {A. Gelman and J. B. Carlin and H. S. Stern and D. B. Rubin},
  title     = {Bayesian data analysis},
  publisher = {Chapman and Hall/CRC},
  year      = 1995,
  address   = {Boca Raton}
}

@InProceedings{gelman96,
  author    = {A. Gelman},
  editor    = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  title     = {Inference and monitoring convergence},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  publisher = {Chapman and Hall},
  year      = 1996,
  pages     = {131--143}
}

@Article{gelman98,
  author    = {A. Gelman},
  title     = {Simulating normalizing constants: {F}rom importance sampling to bridge sampling to path sampling},
  journal   = {Statistical Science},
  year      = 1998,
  volume    = 13,
  pages     = {163--185}
}

@book{gelman03,
    author = "Andrew Gelman and John B. Carlin and Hal S. Stern and Donald B. Rubin",
    title = "Bayesian Data Analysis",
    year = "2003",
    publisher = "Chapman and Hall",
    edition = "second"
}

@Article{gernhard08,
  author    = {T. Gernhard},
  title     = {The conditioned reconstructed process},
  journal   = {Journal of Theoretical Biology},
  year      = 2008,
  volume    = 253,
  pages     = {769--778}
}


@Article{geuten07,
  author    = {W. Geuten and T. Massingham and P. Darius and E. Smets and N. Goldman},
  title     = {Experimental design criteria in phylogenetics: {W}here to add taxa},
  journal   = {Systematic Biology},
  year      = 2007,
  volume    = 56,
  pages     = {609--622}
}

@InProceedings{geyer91,
  author    = {C. J. Geyer},
  editor    = {E. M. Kerimidas},
  title     = {{M}arkov chain {M}onte {C}arlo maximum likelihood},
  booktitle = {Computing Science and Statistics: Proceedings of the 23rd Symposium on the Interface},
  publisher = {Fairfax Station: Interface Foundation},
  year      = 1991,
  pages     = {156--163}
}

@InProceedings{geyer99,
  author    = {C. J. Geyer},
  editor    = {O. E. Barndorff-Nielsen and W. S. Kendall and M. N. M. van Lieshout},
  title     = {Likelihood inference for spatial point processes},
  booktitle = {Stochastic {G}eometry: {L}ikelihood and {C}omputation},
  publisher = {Chapman and Hall/CRC},
  year      = 1999,
  pages     = {79--140}
}

@Article{gilbert86,
  author    = {W. Gilbert},
  title     = {The {RNA} world},
  journal   = {Nature},
  year      = 1986,
  volume    = 319,
  pages     = {618}
}

@Article{gilks94,
  author    = {W. R. Gilks and A. Thomas and D. J. Spiegelhalter},
  title     = {A language and program for complex {B}ayesian modelling},
  journal   = {The Statistician},
  year      = 1994,
  volume    = 43,
  pages     = {169--177}
}

@Book{gilks96a,
  editor    = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  title     = {Markov chain {M}onte {C}arlo in practice},
  publisher = {Chapman and Hall/CRC},
  year      = 1996,
  address   = {Boca Raton}
}

@InProceedings{gilks96b,
  author    = {W. R. Gilks},
  editor    = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  title     = {Full conditional distributions},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  publisher = {Chapman and Hall},
  year      = 1996,
  pages     = {75--88}
}

@InProceedings{gilks96c,
  author    = {W. R. Gilks and G. O. Roberts},
  editor    = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  title     = {Strategies for improving {MCMC}},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  publisher = {Chapman and Hall},
  year      = 1996,
  pages     = {89--114}
}

@Article{golding83,
  author    = {G. B. Golding},
  title     = {Estimates of {DNA} and protein sequence divergence: {A}n examination of some assumptions},
  journal   = {Molecular Biology and Evolution},
  year      = 1983,
  volume    = 1,
  pages     = {125--142}
}

@Article{goldman90,
  author    = {N. Goldman},
  title     = {Maximum likelihood inference of phylogenetic trees with special reference to a {P}oisson process model of {DNA} substitution and to parsimony analyses},
  journal   = {Systematic Zoology},
  year      = 1990,
  volume    = 39,
  pages     = {345--361}
}

@Article{goldman93,
  author    = {N. Goldman},
  title     = {Statistical tests of models of {DNA} substitution},
  journal   = {Journal of Molecular Evolution},
  year      = 1993,
  volume    = 36,
  pages     = {182--198}
}

@Article{goldman94,
  author    = {N. Goldman and Z. Yang},
  title     = {A codon-based model of nucleotide substitution for protein-coding {DNA} sequences},
  journal   = {Molecular Biology and Evolution},
  year      = 1994,
  volume    = 11,
  pages     = {725--736}
}

@Article{goldman96,
  author    = {N. Goldman and J. Thorne and D. Jones},
  title     = {Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses},
  journal   = {Journal of Molecular Biology},
  year      = 1996,
  volume    = 263,
  pages     = {196--208}
}

@Article{goldstein06,
  author    = {R. N. Goldstein},
  title     = {Architectural design and the collaborative research environment},
  journal   = {Cell},
  year      = 2006,
  volume    = 127,
  pages     = {243--246}
}

@article{goloboff03,
  author    = {P. A. Goloboff},
  title     = {Parsimony, likelihood, and simplicity},
  journal   = {Cladistics},
  year      = 2003,
  volume    = 19,
  pages     = {91--103}
}

@Book{golub83,
  author    = {G. H. Golub and C. F. Van Loan},
  title     = {Matrix {C}omputations},
  publisher = {Johns Hopkins University Press},
  year      = 1983,
  address   = {Baltimore, Maryland}
}

@article{gotoh82,
  author    = {O. Gotoh},
  title     = {An improved algorithm for matching biological sequences},
  journal   = JMB,
  year      = 1982,
  volume    = 162,
  pages     = {705--708}
}

@Article{graham00,
  author    = {M. Graham and J. Kennedy and C. Hand},
  title     = {A comparison of set-based and graph-based visualisations of overlapping classification hierarchies},
  journal   = {Proceedings of Advanced Visual Interfaces},
  year      = 2000,
  pages     = {41--50}
}

@Article{grantham74,
  author    = {R. Grantham},
  title     = {Amino acid difference formula to help explain protein evolution},
  journal   = {Science},
  year      = 1974,
  volume    = 185,
  pages     = {862--864}
}

@Article{graybeal94,
  author    = {A. Graybeal},
  title     = {Evaluating the phylogenetic utility of genes: {A} search for genes informative about deep divergences among vertebrates},
  journal   = {Systematic Biology},
  year      = 1994,
  volume    = 43,
  pages     = {174--193}
}

@Article{green95,
  author    = {P. J. Green},
  title     = {Reversible jump {MCMC} computation and {B}ayesian model determination},
  journal   = {Biometrika},
  year      = 1995,
  volume    = 82,
  pages     = {771--732}
}

@InProceedings{green03,
  author    = {P. J. Green},
  editor    = {P. J. Green and N. L. Hjort and S. Richardson},
  title     = {Trans-dimensional {M}arkov chain {M}onte {C}arlo},
  booktitle = {Highly {S}tructured {S}tochastic {S}ystems},
  publisher = {Oxford University Press},
  year      = 2003,
  pages     = {179--198}
}

@Article{green08,
  author    = {R. E. Green and A.-S. Malaspinas and J. Krause and A. W. Briggs and P. L. F. Johnson and C. Uhler and M. Meyer and J. M. Good and T. Maricic and U. Stenzel and K. Pr\"ufer and M. Siebauer and H. A. Burbano and M. Ronan and J. M. Rothberg and M. Egholm and P. Rudan and D. Brajkovi\'c and \u{Z}. Ku\'can and I. Gu\u{s}i\'c and M. Wikstr\"om and L. Laakkonen and J. Kelso and M. Slatkin and S. P\"a\"abo},
  title     = {A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing},
  journal   = {Cell},
  year      = 2008,
  volume    = 134,
  pages     = {416--426}
}

@Article{greider85,
  author    = {C. W. Greider and E. H. Blackburn},
  title     = {Identification of a specific telomere terminal transferase activity in {T}etrahymena extracts},
  journal   = {Cell},
  year      = 1985,
  volume    = 43,
  pages     = {405--413}
}

@Article{gu95,
  author    = {X. Gu and Y. -X. Fu and W.-H. Li},
  title     = {Maximum likelihood estimation of the heterogeneity of substitution rates among nucleotide sites},
  journal   = {Molecular Biology and Evolution},
  year      = 1995,
  volume    = 12,
  pages     = {546--557}
}

@Article{guindon04,
  author    = {S. Guindon and A. G. Rodrigo and K. A. Dyer and J. P. Huelsenbeck},
  title     = {Modeling the site-specific variation of selection patterns along lineages},
  journal   = {Proceedings of the National Academy of Science, U.S.A.},
  year      = 2004,
  volume    = 101,
  pages     = {12957--12962}
}

@Article{gusfield02,
  author    = {D. Gusfield},
  title     = {Partition-distance: a problem and class of perfect graphs arising in clustering},
  journal   = {Information Processing Letters},
  year      = 2002,
  volume    = 82,
  pages     = {159--164}
}

@InProceedings{gutell96,
  author    = {R. R. Gutell},
  editor    = {A. E. Dahlberg and R. A. Zimmermann},
  title     = {Comparative sequence analysis and the structure of {16S} and {23S} {rRNA}},
  booktitle = {Ribosomal RNA: Structure, Evolution, Processing and Function in Protein Biosynthesis},
  publisher = {CRC Press},
  year      = 1996,
  pages     = {111--128}
}

@Article{gutell02,
  author    = {R. R. Gutell and J. C. Lee and J. J. Cannone},
  title     = {The accuracy of ribosomal {RNA} comparative structure models},
  journal   = {Current Opinion in Structural Biology},
  year      = 2002,
  volume    = 12,
  pages     = {301--310}
}

@Article{guyer91,
  author    = {C. Guyer and J. B. Slowinski},
  title     = {Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages},
  journal   = {Evolution},
  year      = 1991,
  volume    = 45,
  pages     = {340--350}
}


%*********************************************************************************
% H
%*********************************************************************************

@Book{haeckel66,
  author    = {E. Haeckel},
  title     = {Generelle {M}orphologie der {O}rganismen: {A}llgemeine {G}rundzuge der organischen {F}ormen-{W}issenschaft, 
               mechanisch begrundet durch die von {C}harles {D}arwin reformirte {D}escendenz-{T}heorie},
  publisher = {Georg Riemer},
  year      = 1866,
  address   = {Berlin}
}

@Article{hafner94,
  author    = {M. S. Hafner and P. D. Sudman and F. X. Villablanca and T. A. Spradling and J. W. Demastes and S. A. Nadler},
  title     = {Disparate rates of molecular evolution in cospeciating hosts and parasites},
  journal   = {Science},
  year      = 1994,
  volume    = 265,
  pages     = {1087--1090}
}

@Article{hahn00,
  author    = {B. H. Hahn and G. M. Shaw and K. M. de Cock and P. M. Sharp},
  title     = {{AIDS} as a zoonosis: {S}cientific and public health implications},
  journal   = {Science},
  year      = 2000,
  volume    = 287,
  pages     = {607--614}
}

@Article{hall06,
  author    = {B. G. Hall},
  title     = {Simple  and accurate estimation of ancestral protein sequences},
  journal   = {Proceedings of the National Academy of  Science, U.S.A.},
  year      = 2006,
  volume    = 103,
  pages     = {5431--5436}
}

@Article{harshman03,
  author    = {J. Harshman and C. J. Huddleston and J. P. Bollback and T. J. Parsons and M. J. Braun},
  title     = {True and false {G}harials: a nuclear gene phylogeny of {C}rocodylia},
  journal   = {Systematic Biology},
  year      = 2003,
  volume    = 52,
  pages     = {386--402}
}

@Article{hartigan73,
  author    = {J. A. Hartigan},
  title     = {Minimum mutation fits to a given tree},
  journal   = {Biometrics},
  year      = 1973,
  volume    = 29,
  pages     = {53--65}
}

@Article{hartmann10,
  author    = {K. Hartmann and D. Wong and T. Stadler},
  title     = {Sampling trees from evolutionary models},
  journal   = {Systematic Biology},
  year      = 2010,
  volume    = 59,
  pages     = {465--476}
}

@Book{harvey91,
  author    = {P. H. Harvey and M. D. Pagel},
  title     = {The {C}omparative {M}ethod in {E}volutionary {B}iology},
  publisher = {Oxford University Press},
  year      = 1991,
  address   = {Oxford}
}

@Article{hasegawa84,
  author    = {M. Hasegawa and T. Yano and H. Kishino},
  title     = {A new molecular  clock of mitochondrial {DNA} and the evolution of {H}ominoids},
  journal   = {Proc. Japan Acad. Ser. B},
  year      = 1984,
  volume    = 60,
  pages     = {95--98}
}

@Article{hasegawa85,
  author    = {M. Hasegawa and H. Kishino and T. Yano},
  title     = {Dating the human-ape splitting by a molecular clock of mitochondrial {DNA}},
  journal   = {Journal of Molecular Evolution},
  year      = 1985,
  volume    = 22,
  pages     = {160--174}
}

@Article{hasegawa91,
  author    = {M. Hasegawa and J. Horai},
  title     = {Time of the deepest root for polymorphism in human mitochondrial {DNA}},
  journal   = {Journal of Molecular Evolution},
  year      = 1991,
  volume    = 32,
  pages     = {37--42}
}

@Article{hastings70,
  author    = {W. K. Hastings},
  title     = {{Monte Carlo} sampling methods using {Markov} chains and their applications},
  journal   = {Biometrika},
  year      = 1970,
  volume    = 57,
  pages     = {97--109}
}

@Article{hayasaka88,
  author    = {K. Hayasaka and T. Gojobori and S. Horai},
  title     = {Molecular phylogeny and evolution of primate mitochondrial {DNA}},
  journal   = {Molecular Biology and Evolution},
  year      = 1988,
  volume    = 5,
  pages     = {626--644}
}

@Article{heerwagen04,
  author    = {J. H. Heerwagen and K. Kampschoer and K. M. Powell and V. Loftness},
  title     = {Collaborative knowledge work environments},
  journal   = {Building Research \& Information},
  year      = 2004,
  volume    = {32},
  pages     = {510--528}
}

@Article{hein00,
  author    = {J. Hein and C. Wiuf and B. Knudsen and M. B. Moller and G. Wibling},
  title     = {Statistical alignment: computational properties, homology testing and goodness-of-fit},
  journal   = JMB,
  year      = 2000,
  volume    = {302},
  pages     = {265--279}
}

@InProceedings{hein01,
  author    = {J. Hein},
  title     = {An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree},
  booktitle = {Pacific Symposium on Biocomputing},
  pages     = {179--190},
  year      = {2001},
  editor    = {R. B. Altman and A. K. Dunker and L. Hunter and K. Lauderdale and T. E. Klein},
  publisher = {World Scientific},
  address   = {Singapore}
}

@Article{hein03,
   Author   = "J. Hein and J. L. Jensen and C. N. S. Pedersen",
   Title    = "{{R}ecursions for statistical multiple alignment}",
   Journal  = PNAS,
   Year     = "2003",
   Volume   = "100",
   Number   = "25",
   Pages    = "14960--14965",
   Month    = "Dec"
}

@Article{hendy93,
  author    = {M. D. Hendy and D. Penny},
  title     = {Spectral analysis of phylogenetic data},
  journal   = {Journal of Classification},
  year      = 1993,
  volume    = 10,
  pages     = {5--24}
}

@Article{henikoff92,
  author    = {S. Henikoff and J. G. Henikoff},
  title     = {Amino acid substitution matrices from  protein blocks},
  journal   = {Proceedings of the National Academy of Science, U.S.A.},
  year      = 1992,
  volume    = 89,
  pages     = {10915--10919}
}

@Book{hennig50,
  author    = {W. Hennig},
  title     = {Grundzuge einer {T}heorie der {P}hylogenetischen {S}ystematik},
  publisher = {Deutscher Zentralverlag},
  year      = 1950,
  address   = {Berlin}
}

@Book{hennig66,
  author    = {W. Hennig},
  title     = {Phylogenetic {S}ystematics},
  publisher = {University of Illinois Press},
  year      = 1966,
  address   = {Urbana}
}

@Book{hennig69,
  author    = {W. Hennig},
  title     = {Die {S}tammesgeschichte der {I}nsekten},
  publisher = {Kramer},
  year      = 1969,
  address   = {Frankfurt}
}

@Article{herman00,
  author    = {I. Herman and G. Melancon and M. S. Marshall},
  title     = {Graph visualization and navigation in information visualization: {A} survey},
  journal   = {IEEE Transactions on Visualization and Computer Graphics},
  year      = 2000,
  volume    = 6,
  pages     = {24--43}
}

@Article{hess94,
  author    = {S. T. Hess and J. D. Blake and R. D. Blake},
  title     = {Wide variations in neighbor-dependent substitution rates},
  journal   = {JMB},
  year      = 1994,
  volume    = 236,
  pages     = {1022--1033}
}

@Article{hey07,
  author    = {J. Hey and R. Nielsen},
  title     = {Integration with the {F}elsenstein equation for improved {M}arkov chain {M}onte {C}arlo methods in population genetics},
  journal   = {Proceedings of the National Academy of Science, U.S.A.},
  year      = 2007,
  volume    = 104,
  pages     = {2785--2790}
}

@Article{higgins88,
  author    = {D. G. Higgins and P. M. Sharp},
  title     = {{CLUSTAL}---a package for performing multiple sequence alignment on a microcomputer},
  journal   = {Gene},
  year      = 1988,
  volume    = 73,
  pages     = {237--244}
}

@InProceedings{hillis94,
  author    = {D. M. Hillis},
  editor    = {B. K. Hall},
  title     = {Homology in molecular biology},
  booktitle = {Homology: {T}he {H}ierarchical {B}asis of {C}omparative {B}iology},
  publisher = {Academic Press},
  year      = 1994,
  pages     = {339--368}
}

@Article{hillis96,
  author    = {D. M. Hillis},
  title     = {Inferring complex phylogenies},
  journal   = {Nature},
  year      = 1996,
  volume    = 383,
  pages     = {130--131}
}

@Article{hitchcock03,
  author    = {D. Hitchcock},
  title     = {A history of the {M}etropolis-{H}astings algorithm},
  journal   = {The American Statistician},
  year      = 2003,
  volume    = 57,
  pages     = {254--257}
}

@Article{hogeweg84,
  author    = {P. Hogeweg and P. Hesper},
  title     = {The alignment of sets of sequences and the construction of phyletic trees: {A}n integrated method},
  journal   = {Journal of Molecular Evolution},
  year      = 1984,
  volume    = 20,
  pages     = {175--186}
}

@article{holder03,
  author    = {M. T. Holder and P. O. Lewis},
  title     = {Phylogeny estimation: {T}raditional and {B}ayesian approaches.},
  journal   = {Nature Reviews Genetics},
  year      = 2003,
  volume    = 4,
  pages     = {275--284}
}

@article{holder10,
  author    = {M. T. Holder and P. O. Lewis and D. L. Swofford},
  title     = {The {A}kaike information criterion will not choose the no common mechanism model},
  journal   = {Systematic Biology},
  year      = 2010,
  volume    = 59,
  number    = 4,
  pages     = {477--485}
}

@article{holmes98,
  author    = {I. Holmes and R. Durbin},
  title     = {Dynamic programming alignment accuracy},
  journal   = JCB,
  year      = 1998,
  volume    = 5,
  number    = 3,
  pages     = {493--504}
}

@article{holmes01,
  author    = {I. Holmes and W. J. Bruno},
  title     = {Evolutionary {HMM}s: a {B}ayesian approach to multiple alignment},
  year      = 2001,
  journal   = BI,
  volume    = 17,
  number    = 9,
  pages     = {803--820}
}

@article{holmes03,
  author    = {I. Holmes},
  title     = {Using guide trees to construct multiple-sequence evolutionary {HMM}s},
  journal   = BI,
  volume    = "19 Suppl. 1",
  pages     = {i147--157},
  year      = 2003
}

@Article{holmes04,
  author    = {I. Holmes},
  title     = {A probabilistic model for the evolution of {RNA} structure},
  journal   = BMCBI,
  year      = 2004,
  volume    = 5,
  number    = 166
}

@Article{holmes05,
  author    = {I. Holmes},
  title     = {Accelerated probabilistic inference of {RNA} structure evolution},
  journal   = BMCBI,
  year      = 2005,
  volume    = 6,
  number    = 73
}

@Article{holmes05b,
  author    = {I. Holmes},
  title     = {Using evolutionary {E}xpectation {M}aximization to estimate indel rates},
  journal   = BI,
  year      = 2005,
  volume    = 21,
  number    = 10,
  pages     = {2294--2300}
}

@Article{holmes07,
  Author    = "I. Holmes",
  Title     = "{{P}hylocomposer and {P}hylodirector: {A}nalysis and {V}isualization of {T}ransducer {I}ndel {M}odels}",
  Journal   = BI,
  Year      = "2007",
  Month     = "Sep"
}

@Unpublished{holmes02a,
  author    = {I. Holmes and G. M. Rubin},
  title     = {Pairwise {RNA} structure comparison using stochastic context-free grammars},
  note      = {Pacific Symposium on Biocomputing, 2002},
  year      = 2002
}

@Article{holmes02b,
  author    = {I. Holmes and G. M. Rubin},
  title     = {An {E}xpectation {M}aximization algorithm for training hidden substitution models},
  journal   = JMB,
  volume    = 317,
  number    = 5,
  pages     = {757--768},
  year      = 2002
}

@Article{horner19,
  author    = {W. G. Horner},
  title     = {A new method of solving numerical equations of all orders, by continuous approximation},
  journal   = {Philosophical Transactions of the Royal Society of London},
  year      = 1819,
  volume    = 109,
  pages     = {308--335}
}

@Book{howson93,
  author    = {C. Howson and P. Urbach},
  title     = {Scientific {R}easoning: {T}he {B}ayesian {A}pproach, {S}econd {E}dition},
  publisher = {Open Court},
  year      = 1993,
  address   = {Chicago}
}

@Article{hudson90,
  author    = {R. R. Hudson},
  title     = {Gene genealogies and the coalescent process},
  journal   = {Oxford Surveys in Evolutionary Biology},
  year      = 1990,
  volume    = 7,
  pages     = {1--44}
}

@Article{huelsenbeck93,
  author    = {J. P. Huelsenbeck and D. M. Hillis},
  title     = {Success of phylogenetic methods in the four-taxon case},
  journal   = {Systematic Biology},
  year      = 1993,
  volume    = 42,
  pages     = {247--264}
}

@Article{huelsenbeck95a,
  author    = {J. P. Huelsenbeck},
  title     = {Performance of phylogenetic methods in simulation},
  journal   = {Systematic Biology},
  year      = 1995,
  volume    = 44,
  pages     = {17--48}
}

@Article{huelsenbeck95b,
  author    = {J. P. Huelsenbeck},
  title     = {The robustness of two phylogenetic methods: {F}our taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining},
  journal   = {Molecular Biology and Evolution},
  year      = 1995,
  volume    = 12,
  pages     = {843--849}
}

@Article{huelsenbeck96a,
  author    = {J. P. Huelsenbeck and M. Kirkpatrick},
  title     = {Do phylogenetic methods produce trees with biased shapes?},
  journal   = {Evolution},
  year      = 1996,
  volume    = 50,
  pages     = {1418--1424}
}

@Article{huelsenbeck96b,
  author    = {J. P. Huelsenbeck and J. J. Bull},
  title     = {A likelihood ratio test for detection of conflicting phylogenetic signal},
  journal   = {Systematic Biology},
  year      = 1996,
  volume    = 45,
  pages     = {92--98}
}

@Article{huelsenbeck96c,
  author    = {J. P. Huelsenbeck and J. J. Bull and C. W. Cunningham},
  title     = {Combining data in phylogenetic analysis},
  journal   = {Trends in Ecology and Evolution},
  year      = 1996,
  volume    = 11,
  pages     = {152--158}
}

@Article{huelsenbeck96d,
  author    = {J. P. Huelsenbeck and D. M. Hillis and R. Nielsen},
  title     = {A likelihood-ratio test of monophyly},
  journal   = {Systematic Biology},
  year      = 1996,
  volume    = 45,
  pages     = {546--558}
}

@Article{huelsenbeck97a,
  author    = {J. P. Huelsenbeck and B. Rannala},
  title     = {Phylogenetic methods come of age: {T}esting hypotheses in an evolutionary context},
  journal   = {Science},
  year      = 1997,
  volume    = 276,
  pages     = {227--232}
}

@Article{huelsenbeck97b,
  author    = {J. P. Huelsenbeck},
  title     = {Is the {F}elsenstein zone a fly trap?},
  journal   = {Systematic Biology},
  year      = 1997,
  volume    = 46,
  pages     = {69--74}
}

@Article{huelsenbeck98,
  author    = {J. P. Huelsenbeck},
  title     = {Systematic bias in phylogenetic analysis: {I}s the {S}trepsiptera problem solved?},
  journal   = {Systematic Biology},
  year      = 1998,
  volume    = 47,
  pages     = {519--537}
}

@Article{huelsenbeck99,
  author    = {J. P. Huelsenbeck and R. Nielsen},
  title     = {Effect of non-independent substitution on phylogenetic accuracy},
  journal   = {Systematic Biology},
  year      = 1999,
  volume    = 48,
  pages     = {317--328}
}

@Article{huelsenbeck00a,
  author    = {J. P. Huelsenbeck and B. Larget and D. L. Swofford},
  title     = {A compound Poisson process for relaxing the molecular clock},
  journal   = {Genetics},
  year      = 2000,
  volume    = 154,
  pages     = {1879--1892}
}

@Article{huelsenbeck00b,
  author    = {J. P. Huelsenbeck and B. Rannala and B. Larget},
  title     = {A {B}ayesian framework for the analysis of cospeciation},
  journal   = {Evolution},
  year      = 2000,
  volume    = 54,
  pages     = {353--364}
}

@Article{huelsenbeck01a,
  author    = {J. P. Huelsenbeck and J. P. Bollback},
  title     = {Empirical and hierarchical bayesian estimation of ancestral states},
  journal   = {Systematic Biology},
  year      = 2001,
  volume    = 50,
  pages     = {351--366}
}

@Article{huelsenbeck01b,
  author    = {J. P. Huelsenbeck and F. Ronquist and R. Nielsen and J. Bollback},
  title     = {{B}ayesian inference of phylogeny and its impact on evolutionary biology},
  journal   = {Science},
  year      = 2001,
  volume    = 294,
  pages     = {2310--2314}
}

@Article{huelsenbeck01c,
  author    = {J. P. Huelsenbeck and F. Ronquist},
  title     = {{MRBAYES}: {B}ayesian inference of phylogenetic trees},
  journal   = {Bioinformatics},
  year      = 2001,
  volume    = 17,
  pages     = {754--755}
}

@Article{huelsenbeck02a,
  author    = {J. P. Huelsenbeck},
  title     = {Testing a covariotide model of DNA substitution},
  journal   = {Molecular Biology and Evolution},
  year      = 2002,
  volume    = 19,
  pages     = {698--707}
}

@Article{huelsenbeck02b,
  author    = {J. P. Huelsenbeck and J. P. Bollback and A. M. Levine},
  title     = {Inferring the root of a phylogenetic tree},
  journal   = {Systematic Biology},
  year      = 2002,
  volume    = 51,
  pages     = {32--43}
}

@Article{huelsenbeck03,
  author    = {J. P. Huelsenbeck and R. Nielsen and J. P. Bollback},
  title     = {Stochastic mapping of morphological characters},
  journal   = {Systematic Biology},
  year      = 2003,
  volume    = 52,
  pages     = {131--158}
}

@Article{huelsenbeck03b,
  author    = {J. P. Huelsenbeck and K. M. Lander},
  title     = {Frequent inconsistency of parsimony under a simple model of cladogenesis},
  journal   = {Systematic Biology},
  year      = 2003,
  volume    = 52,
  pages     = {641--648}
}

@Article{huelsenbeck02c,
  author    = {J. P. Huelsenbeck and N. S. Imennov},
  title     = {Geographic origin of human mitochondrial {DNA}: {A}ccommodating phylogenetic uncertainty and model comparison},
  journal   = {Systematic Biology},
  year      = 2002,
  volume    = 51,
  pages     = {155--165}
}

@InProceedings{huelsenbeck05a,
  author    = {J. P. Huelsenbeck and F. Ronquist},
  editor    = {R. Nielsen},
  booktitle = {Statistical {M}ethods in {M}olecular {E}volution},
  title     = {{B}ayesian Analysis of molecular evolution using {MrBayes}},
  publisher = {Springer-Verlag},
  year      = 2005
}

@Article{huelsenbeck04b,
  author    = {J. P. Huelsenbeck and B. Rannala},
  title     = {Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models},
  journal   = {Systematic Biology},
  year      = 2004,
  volume    = 53,
  pages     = {904--913}
}

@Article{huelsenbeck04c,
  author    = {J. P. Huelsenbeck and K. Dyer},
  title     = {Bayesian estimation of positively selected sites},
  journal   = {Journal of Molecular Evolution},
  year      = 2004,
  volume    = 58,
  pages     = {661--672}
}

@Article{huelsenbeck04d,
  author    = {J. P. Huelsenbeck and B. Larget and M. E. Alfaro},
  title     = {Bayesian phylogenetic model selection using reversible jump {M}arkov chain {M}onte {C}arlo},
  journal   = {Molecular Biology and Evolution},
  year      = 2004,
  volume    = 21,
  pages     = {1123--1133}
}

@InProceedings{huelsenbeck05,
  author    = {J. P. Huelsenbeck and F. Ronquist},
  editor    = {R. Nielsen},
  title     = {Bayesian analysis of molecular evolution using {MrBayes}},
  booktitle = {Statistical Methods in Molecular Evolution},
  publisher = {Springer-Verlag},
  year      = 2005,
  pages     = {183--232}
}

@Article{huelsenbeck06,
  author    = {J. P. Huelsenbeck and S. Jain and S. W. D. Frost and S. L. Kosakovsky Pond},
  title     = {A {D}irichlet process model for detecting positive selection in protein-coding {DNA} sequences},
  journal   = {Proceedings of the National Academy of Science, U.S.A.},
  year      = 2006,
  volume    = 103,
  pages     = {6263--6268}
}

@Article{huelsenbeck07a,
  author    = {J. P. Huelsenbeck and P. Andolfatto},
  title     = {Inference of population structure under a {D}irichlet process model},
  journal   = {Genetics},
  year      = 2007,
  volume    = 175,
  pages     = {1787--1802}
}

@Article{huelsenbeck07b,
  author    = {J. P. Huelsenbeck and M. Suchard},
  title     = {A Nonparametric Method for Accommodating and Testing Across-Site Rate Variation},
  journal   = {Systematic Biology},
  year      = 2007,
  volume    = 56,
  pages     = {975--987}
}

@Article{huelsenbeck08a,
  author    = {J. P. Huelsenbeck and C. An\'e and B. Larget and F. Ronquist},
  title     = {A {B}ayesian perspective on a non-parsimonious parsimony model},
  journal   = {Systematic Biology},
  year      = 2008,
  volume    = 57,
  pages     = {406--419}
}

@Article{huelsenbeck08b,
  author    = {J. P. Huelsenbeck and P. Joyce and C. Lakner and F. Ronquist},
  title     = {Bayesian analysis of amino acid substitution models},
  journal   = {Proceedings of the Royal Society of London, B},
  year      = {2008},
  volume    = 363,
  pages     = {3941--3953}
}

@Book{hull88,
  author    = {D. L. Hull},
  title     = {Science as a {P}rocess.  {A}n {E}volutionary {A}ccount of the  {S}ocial and {C}onceptual 
               {D}evelopment of {S}cience},
  publisher = {University of Chicago Press},
  year      = 1988,
  address   = {Chicago}
}

@Article{hunt07,
  author    = {T. Hunt and J. Bergsten and Z. Levkanicova and A. Papadopoulou and O. St. John and R. Wild and P. M. Hammond and D. Ahrens and M. Balke and M. S. Caterino and J. G\'omez-Zurita and I. Ribera and T. G. Barraclough and M. Bocakova and L. Bocak and A. P. Vogler},
  title     = {A comprehensive phylogeny of {B}eetles reveals the evolutionary origins of a superradiation},
  journal   = {Science},
  year      = 2007,
  volume    = 318,
  pages     = {1913--1916}
}

%*********************************************************************************
% I
%*********************************************************************************

@Article{ihaka96,
  author    = {R. Ihaka and R. Gentleman},
  title     = {R: {A} Language for data analysis and graphics},
  journal   = {Journal of Computational and Graphical Statistics},
  year      = 1996,
  volume    = 5,
  pages     = {299--314}
}

%*********************************************************************************
% J
%*********************************************************************************

@Article{jackman99,
  author    = {T. R. Jackman and A. Larson and K. de Queiroz and J. B. Losos},
  title     = {Phylogenetic relationshiops ad tempo of early diversification in {\it {A}nolis} lizards},
  journal   = {Systematic Biology},
  year      = 1999,
  volume    = 48,
  pages     = {254--285}
}

@Article{jain02,
  author    = {R. Jain and M. Rivera and J. Moore and J. Lake},
  title     = {Horizontal gene transfer in microbial genome evolution},
  journal   = {Theoretical Population Biology},
  year      = 2002,
  volume    = 61,
  pages     = {489--495}
}

@Article{jain99,
  author    = {R. Jain and M. Rivera and J. Lake},
  title     = {Horizontal gene transfer among genomes: the complexity hypothesis},
  journal   = {Proceedings of the National Academy of Sciences, USA},
  year      = 1999,
  volume    = 96,
  pages     = {3801--3806}
}

@Article{jain04,
  author    = {S. Jain and R. M. Neal},
  title     = {A split-merge {M}arov chain {M}onte {C}arlo procedure for the {D}irichlet process mixture model},
  journal   = {Journal of Computational and Graphical Statistics},
  year      = 2004,
  volume    = 13,
  pages     = {158--182}
}

@Article{jain07,
  author    = {S. Jain and R. M. Neal},
  title     = {Splitting and merging components of a nonconjugate {D}irichlet process mixture model},
  journal   = {Bayesian analysis},
  year      = 2007,
  volume    = 2,
  pages     = {445--473}
}

@InProceedings{jefferies79,
  author    = {R. P. S. Jefferies},
  editor    = {M. R. House},
  title     = {The origin of chordates --- a methodological essay},
  booktitle = {The {O}rigin of {M}ajor {I}nvertebrate {G}roups},
  publisher = {Academic Press},
  year      = 1979,
  pages     = {443--477}
}

@Article{jeffreys35,
  author    = {H. Jeffreys},
  title     = {Some tests of significance, treated by the theory of probability},
  journal   = {Proceedings of the Cambridge Philosophy Society},
  year      = 1935,
  volume    = 31,
  pages     = {203--222}
}

@Book{jeffreys61,
  author    = {H. Jeffreys},
  title     = {Theory of {P}robability},
  publisher = {Oxford University Press},
  year      = 1961,
  address   = {Oxford}
}

@Article{jermann95,
  author    = {T. M. Jermann and J. G. Opitz and J. Stackhouse and S. A. Benner },
  title     = {Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily},
  journal   = {Nature},
  year      = 1995,
  volume    = 374,
  pages     = {108--110}
}

@Article{jin90,
  author    = {L. Jin and M. Nei},
  title     = {Limitations of the evolutionary parsimony method of phylogenetic analysis},
  journal   = {Molecular Biology and Evolution},
  year      = 1990,
  volume    = 7,
  pages     = {82--102}
}

@Article{jin91,
  author    = {L. Jin and M. Nei},
  title     = {Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data},
  journal   = {Molecular Biology and Evolution},
  year      = 1991,
  volume    = 8,
  pages     = {356--365}
}

@Article{jones92,
  author    = {D. T. Jones and W. R. Taylor and J. M. Thornton},
  title     = {The rapid generation of mutation data matrices from protein sequences},
  journal   = {Computer Applications in the Biosciences (CABIOS)},
  year      = 1992,
  volume    = 8,
  pages     = {275--282}
}

@Article{jones96,
  author    = {D. T. Jones and J. M. Thornton},
  title     = {Potential energy functions for threading},
  journal   = {Curr. Opin. Struct. Biol.},
  year      = 1996,
  volume    = 6,
  pages     = {210--216}
}

@Article{jordan04,
  author    = {M. I. Jordan},
  title     = {Graphical models},
  journal   = {Statistical Science},
  year      = 2004,
  volume    = 19,
  pages     = {140--155}
}

@Book{joset93,
  author    = {F. Joset and J. Guespin-Michel},
  title     = {Prokaryotic {G}enetics},
  publisher = {Blackwell Scientific Publications},
  year      = 1993,
  address   = {Oxford}
}

@InProceedings{jukes69,
  author    = {T. H. Jukes and C. R. Cantor},
  editor    = {H. N. Munro},
  title     = {Evolution of protein molecules},
  booktitle = {Mammalian {P}rotein {M}etabolism},
  publisher = {Academic Press},
  year      = 1969,
  pages     = {21--123}
}

%*********************************************************************************
% K
%*********************************************************************************

@Article{kashyap74,
  author    = {R. L. Kashyap and S. Subas},
  title     = {Statistical estimation of parameters in a phylogenetic tree using a dynamic model of the substitutional process},
  journal   = {Journal of Theoretical Biology},
  year      = 1974,
  volume    = 47,
  pages     = {75-101}
}

@Article{kass95,
  author    = {R. E. Kass and A. E. Raftery},
  title     = {Bayes factors},
  journal   = {Journal of the American Statistical Association},
  year      = 1995,
  volume    = 90,
  number 	= 430,
  pages     = {773--795}
}

@Article{kathirithamby78,
  author    = {J. Kathirithamby},
  title     = {The effects of stylopisation on the sexual development of {{\it Javesella dubia}} ({K}irschbaum) ({H}omoptera: {D}elphacidae)},
  journal   = {Biological Journal of the Linnean Society},
  year      = 1978,
  volume    = 10,
  pages     = {163--179}
}

@Article{kathirithamby89,
  author    = {J. Kathirithamby},
  title     = {A review of the order {S}trepsiptera},
  journal   = {Systematic Entomology},
  year      = 1989,
  volume    = 14,
  pages     = {41--92}
}

@Article{kathirithamby98,
  author    = {J. Kathirithamby},
  title     = {Introductory remarks},
  journal   = {International Journal of Insect Morphology and Embryology},
  year      = 1998,
  volume    = 27,
  pages     = {1--2}
}

@Article{katoh02,
  author    = {K. Katoh and K. Misawa and K. Kuma and T. Miyata},
  title     = {{MAFFT}: {A} novel method for rapid multiple sequence alignment based on fast {F}ourier transform},
  journal   = {Nucleic Acids Research},
  year      = 2002,
  volume    = 30,
  pages     = {3059--3066}
}

@Article{kawahara09,
  author    = {R. Kawahara and M. Miya and K. Mabuchi and T. J Near and N. Nishida},
  title     = {Stickleback phylogenies resolved: {E}vidence from mitochondrial genomes and 11 nuclear genes},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 2009,
  volume    = 50,
  pages     = {401--404}
}

@Article{kellis03,
  author    = {M. Kellis and N. Patterson and M. Endrizzi and B. Birren and E. S. Lander},
  title     = {Sequencing and comparison of yeast species to identify genes and regulatory elements},
  journal   = {Nature},
  year      = 2003,
  volume    = 423,
  pages     = {241--254}
}

@Article{kendall48,
  author    = {D. G. Kendall},
  title     = {On the generalized ``birth-death'' process},
  journal   = {Annual Review of Mathematical Statistics},
  year      = 1948,
  volume    = 19,
  pages     = {1--15}
}

@Article{keller99,
  author    = {M. P. Keller and B. A. Seifried and P. F. Chance},
  title     = {Molecular evolution of the {CMT1A-REP} region: a human- and chimpanzee-specific repeat},
  journal   = {Molecular Biology and Evolution},
  year      = 1999,
  volume    = 16,
  pages     = {1019--1026}
}

@Article{kidd71,
  author    = {K. K. Kidd and L. A. Sgaramella-Zonta},
  title     = {Phylogenetic analysis: {C}oncepts and methods},
  journal   = {American Journal of Human Genetics},
  year      = 1971,
  volume    = 23,
  pages     = {235--252}
}

@Article{kim08,
  author    = {J. Kim and M. J. Sanderson},
  title     = {Penalized likelihood phylogenetic inference: {B}ridging the parsimony-likelihood gap},
  journal   = {Systematic Biology},
  year      = 2008,
  volume    = 57,
  pages     = {665--674}
}

@Article{kimura80,
  author    = {M. Kimura},
  title     = {A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences},
  journal   = {Journal of Molecular Evolution},
  year      = 1980,
  volume    = 16,
  pages     = {111--120}
}

@Article{kimura81,
  author    = {M. Kimura},
  title     = {Estimation of evolutionary distances between homologous nucleotide sequences},
  journal   = {Proceedings of the National Academy of Sciences, USA},
  year      = 1981,
  volume    = 78,
  pages     = {454--458}
}

@Article{kingman82a,
  author    = {J. F. C. Kingman},
  title     = {The coalescent},
  journal   = {Stochastic Processes and their Applications},
  year      = 1982,
  volume    = 13,
  pages     = {235--248}
}

@InProceedings{kingman82b,
  author    = {J. F. C. Kingman},
  editor    = {G. Koch and F. Spizzichino},
  title     = {Exchangeability and the evolution of large populations},
  booktitle = {Exchangeability in {P}robability and {S}tatistics},
  publisher = {North-Holland},
  year      = 1982,
  pages     = {97--112}
}

@InProceedings{kingman82c,
  author    = {J. F. C. Kingman},
  editor    = {J. Gani and E. J. Hannan},
  title     = {On the genealogy of large populations},
  booktitle = {Essays in {S}tatistical {S}cience: {P}apers in {H}onour of {P. A. P. M}oran, Journal of Applied Probability, Special Volume 19A},
  publisher = {Applied Probability Trust},
  year      = 1982,
  pages     = {27--43}
}

@Article{kinzelbach71,
  author    = {R. K. Kinzelbach},
  title     = {Morphologische Befunde an F{\"a}cherfl{\"u}glern und ihre phylogenetische bedeutung ({I}nsecta: {S}trepsiptera)},
  journal   = {Zoologica},
  year      = 1971,
  volume    = 119,
  pages     = {1--256}
}

@Article{kimura81,
  author    = {M. Kimura},
  title     = {Estimation of evolutionary distances between homologous nucleotide sequences},
  journal   = {Proceedings of the National Academy of Sciences, USA},
  year      = 1981,
  volume    = 78,
  pages     = {454--458}
}

@Article{kirkpatrick93,
  author    = {M. Kirkpatrick and M. Slatkin},
  title     = {Searching for evolutionary patterns in the shape of a phylogenetic tree},
  journal   = {Evolution},
  year      = 1993,
  volume    = 47,
  pages     = {1171--1181}
}

@Article{kishino90,
  author    = {H. Kishino and T. Miyata and M. Hasegawa},
  title     = {Maximum likelihood inference of protein phylogeny and th origin of chloroplasts},
  journal   = {Journal of Molecular Evolution},
  year      = 1990,
  volume    = 31,
  pages     = {151--160}
}

@InProceedings{kishino90b,
  author    = {H. Kishino and M. Hasegawa},
  editor    = {R. F. Doolittle},
  title     = {Converting distance to time: Application to human evolution},
  booktitle = {Methods in Enzymology},
  year      = 1990,
  pages     = {550--5570}
}

@Article{kishino01,
  author    = {H. Kishino and J. L. Thorne and W. Bruno},
  title     = {Performance of a divergence time estimation method under a probabilistic model of rate evolution},
  journal   = {Molecular Biology and Evolution},
  year      = 2001,
  volume    = 18,
  pages     = {352--361}
}

@Book{kolmogorov33,
  author    = {A. N. Kolmogorov},
  title     = {Grundbegriffe der {W}ahrscheinlichkeitsrechnung},
  publisher = {Springer-Verlag},
  year      = 1933,
  address   = {Berlin}
}

@Article{konings87,
  author    = {D. A. Konings and P. Hogeweg and B. Hesper},
  title     = {Evolution of the primary and secondary structures of {E1a} m{RNA}s of the adenovirus},
  journal   = {Molecular Biology and Evolution},
  year      = 1987,
  volume    = 4,
  pages     = {300--314}
}

@Article{kosiol07,
  author    = {Carolin Kosiol and Ian Holmes and Nick Goldman},
  title     = {An empirical codon model for protein sequence evolution},
  journal   = {Molecular Biology and Evolution},
  year      = {2007},
  volume    = {24},
  pages     = {1464--1479}
}

@Article{klosterman06,
  author    = {P. S. Klosterman and A. V. Uzilov and Y. R. Bendana and R. K. Bradley and S. Chao and C. Kosiol and N. Goldman and I. Holmes},
  title     = {{XRate}: a fast prototyping, training and annotation tool for phylo-grammars},
  journal   = BMCBI,
  year      = 2006,
  volume    = 7,
  number    = 428
}

@Article{kluge89,
  author    = {A. G. Kluge},
  title     = {A concern for evidence and a phylogenetic hypothesis of relationships among {E}picarates ({B}oidae, {S}erpentes)},
  journal   = {Systematic Zoology},
  year      = 1989,
  volume    = 14,
  pages     = {151--158}
}

@Article{kluge97a,
  author    = {A. G. Kluge},
  title     = {Testability and the refutation and corroboration of cladistic hypotheses},
  journal   = {Cladistics},
  year      = 1997,
  volume    = 13,
  pages     = {81--96}
}

@Article{kluge97b,
  author    = {A. G. Kluge and J. S. Farris},
  title     = {Quantitative phyletics and the evolution of anurans},
  journal   = {Systematic Zoology},
  year      = 1969,
  volume    = 18,
  pages     = {1--32}
}

@Article{kluge98,
  author    = {A. G. Kluge},
  title     = {Total evidence or taxonomic congruence: {C}ladistics or consensus classification},
  journal   = {Cladistics},
  year      = 1998,
  volume    = 14,
  pages     = {151--158}
}

@Article{kluge69,
  author    = {A. G. Kluge and J. S. Farris},
  title     = {Quantitative phyletics and the evolution of anurans},
  journal   = {Systematic Zoology},
  year      = 1969,
  volume    = 18,
  pages     = {1--32}
}

@Article{kluge93,
  author    = {A. G. Kluge and A. J. Wolf},
  title     = {Cladistics: {W}hat's in a word?},
  journal   = {Cladistics},
  year      = 1993,
  volume    = 9,
  pages     = {183--199}
}

@article{knudsen03,
  author    = {B. Knudsen and M. Miyamoto},
  title     = {Sequence Alignments and Pair Hidden {M}arkov Models Using Evolutionary History},
  journal   = JMB,
  year      = 2003,
  volume    = 333,
  number    = 2,
  pages     = {453--460}
}

@InProceedings{kraut90,
  author    = {R. E. Kraut and C. Egido and J. Galegher},
  editor    = {R. E. Kraut and C. Egido},
  title     = {Patterns of contact and communication in scientific research collaboration},
  booktitle = {Intellectual {T}eamwork},
  publisher = {Earlbaum, Hillsdale},
  year      = 1990
}

@article{krogh97,
  author    = "A. Krogh",
  title     = "Two methods for improving performance of a {HMM} and their application for gene finding",
  journal   = "Proc. Int. Conf. Intell. Syst. Mol. Biol.",
  year      = 1997,
  volume    = 5,
  pages     = "179--186"
}

@Article{kruspe07,
  Author    = "M. Kruspe and P. F. Stadler",
  Title     = "{{P}rogressive multiple sequence alignments from triplets}",
  Journal   = "BMC Bioinformatics",
  Year      = "2007",
  Volume    = "8",
  Pages     = "254"
}

@Article{kuhner94,
  author    = {M. Kuhner and J. Felsenstein},
  title     = {A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates},
  journal   = {Molecular Biology and Evolution},
  year      = 1994,
  volume    = 11,
  pages     = {459--468}
}

@Article{kuhner95,
  author    = {M. Kuhner and J. Yamato and J. Felsenstein},
  title     = {Estimating effective population size and mutation rate from sequence data using {M}etropolis-{H}astings sampling},
  journal   = {Genetics},
  year      = 1995,
  volume    = 140,
  pages     = {1421--1430}
}

@Article{kullback51,
  author    = {S. Kullback and R. A. Leibler},
  title     = {On information and sufficiency},
  journal   = {Annals of Mathematical Statistics},
  year      = 1951,
  volume    = 22,
  pages     = {79--86}
}

%*********************************************************************************
% L
%*********************************************************************************

@Article{lake91,
  author    = {J. A. Lake},
  title     = {The order of sequence alignment can bias the selection of tree topology},
  journal   = {Molecular Biology and Evolution},
  year      = 1991,
  volume    = 8,
  pages     = {378--385}
}

@Article{larget99,
  author    = {B. Larget and D. L. Simon},
  title     = {Markov chain {M}onte {C}arlo algorithms for the {B}ayesian analysis of phylogenetic trees},
  journal   = {Molecular Biology and Evolution},
  year      = 1999,
  volume    = 16,
  pages     = {750--759}
}

@Article{larget05,
  author    = {B. Larget and D. L. Simon and J. B. Kadane},
  title     = {A Bayesian analysis of metazoan mitochondrial genome arrangements},
  journal   = {Molecular Biology and Evolution},
  year      = 2005,
  volume    = 22,
  pages     = {486--495}
}

@Article{larsen93,
  author    = {N. Larsen and C. Zwieb},
  title     = {The signal recognition particle database (SRPDB)},
  journal   = {Nucleic Acids Research},
  year      = 1993,
  volume    = 21,
  pages     = {3019--3020}
}

@Article{li00,
  author    = {S. Li and H. Doss and D. Pearl},
  title     = {Phylogenetic tree reconstruction using {M}arkov chain {M}onte {C}arlo},
  journal   = {Journal of the American Statistical Society},
  year      = 2000,
  volume    = 95,
  pages     = {493--508}
}

@Book{liu01,
  author    = {J. S. Liu},
  title     = {Monte {C}arlo strategies in scientific computing},
  publisher = {Springer},
  year      = 2001,
  address   = {New York}
}

@Article{li00,
  author    = {S. Li and H. Doss and D. Pearl},
  title     = {Phylogenetic tree reconstruction using {M}arkov chain {M}onte {C}arlo},
  journal   = {Journal of the American Statistical Society},
  year      = 2000,
  volume    = 95,
  pages     = {493--508}
}

@Article{lakner08,
  author    = {C. Lakner and P. van der Mark and J. P. Huelsenbeck and B. Larget and F. Ronquist},
  title     = {Efficiency of {MCMC} proposals in {B}ayesian phylogenetics},
  journal   = {Systematic Biology},
  year      = 2008,
  pages     = {86--103}
}

@Article{lamping95,
  author    = {J. Lamping and R. Rao and P. Pirolli},
  title     = {A focus+context technique based on hyperbolic geometry for visualizing large hierarchies},
  journal   = {Proceedings of Human Factors in Computing Systems},
  year      = 1995,
  pages     = {401--408}
}

@Article{lanave84,
  author    = {C. Lanave and G. Preparata and C. Saccone and G. Serio},
  title     = {A new method for calculating evolutionary substitution rates},
  journal   = {Journal of Molecular Evolution},
  year      = 1984,
  volume    = 20,
  pages     = {86--93}
}

@Article{larget98,
  author    = {B. Larget and D. Simon},
  title     = {Faster likelihood calculations on trees},
  journal   = {Technical Report 98-02, Department of Mathematics and Computer Science, Duquesne University, Pittsburgh, Pennsylvania},
  year      = 1998
}

@Article{lavine99,
  author    = {M. Lavine and M. J. Schervish},
  title     = {Bayes factors: {W}hat they are and what they are not},
  journal   = {American Statistician},
  year      = 1999,
  volume    = 53,
  pages     = {119--122}
}

@Article{laplace74,
  author    = {P. S. Laplace},
  title     = {M{\'e}moire sur la probabilit{\'e} des causes le {\'ev\`e}nemens},
  journal   = {M{\'e}moires de l'Acad{\'e}mie Royale des Sciences Present{\'e}s par Divers Savans},
  year      = 1774,
  volume    = 6,
  pages     = {621--656}
}

@Book{laplace12,
  author    = {P. S. Laplace},
  title     = {Th{\'e}orie {A}nalytique des {P}robabilit{\'e}s},
  publisher = {Unknown Publisher},
  year      = 1812,
  address   = {Paris}
}

@Article{lartillot04,
  author    = {N. Lartillot and H. Philippe},
  title     = {A {B}ayesian mixture model for across-site heterogeneities in the amino-acid replacement process},
  journal   = {Molecular Biology and Evolution},
  year      = 2004,
  volume    = 21,
  pages     = {1095--1109}
}

@Article{lartillot06,
  author    = {N. Lartillot and H. Philippe},
  title     = {Computing {B}ayes factors using Theromodynamic integration},
  journal   = {Systematic Biology},
  year      = 2006,
  volume    = 55,
  pages     = {195--207}
}

@Book{lauritzen96,
  author    = {S. L. Lauritzen},
  title     = {Graphical Models},
  publisher = {Clarendon Press},
  year      = 1996,
  address   = {Oxford}
}

@Article{lawrence97,
  author    = {J. Lawrence and H. Ochman},
  title     = {Amelioration of bacterial genomes: rates of change and exchange},
  journal   = {Journal of Molecular Evolution},
  year      = 1997,
  volume    = 44,
  pages     = {383--397}
}

@Article{lawrence99,
  author    = {J. Lawrence},
  title     = {Gene transfer, speciation and the evolution of bacterial genomes},
  journal   = {Current Opinions in Microbiology},
  year      = 1999,
  volume    = 2,
  pages     = {519--523}
}

@Article{lepage07,
  author    = {T. Lepage and D. Bryant and H. Philippe and N. Lartillot},
  title     = {A general comparison of relaxed molecular clock models},
  journal   = {Molecular Biology and Evolution},
  year      = 2007,
  volume    = 24,
  pages     = {2669--2680}
}

@Article{lewis98,
  author    = {P. O. Lewis},
  title     = {A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data},
  journal   = {Molecular Biology and Evolution},
  year      = 1998,
  volume    = 15,
  pages     = {277--283}
}

@Article{lewis01,
  author    = {P. O. Lewis},
  title     = {A likelihood approach to estimating phylogeny from discrete morphological character data},
  journal   = {Systematic Biology},
  year      = 2001,
  volume    = 50,
  pages     = {913--925}
}

@Article{li85,
  author    = {W. -H. Li and C. -I Wu and C. -C Luo},
  title     = {A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes},
  journal   = {Molecular Biology and Evolution},
  year      = 1985,
  volume    = 2,
  pages     = {150--174}
}

@Article{li93,
  author    = {W. -H. Li},
  title     = {Unbiased estimation of the rates of synonymous and nonsynonymous substitution},
  journal   = {Journal of Molecular Evolution},
  year      = 1993,
  volume    = 36,
  pages     = {96--99}
}

@Phdthesis{li96,
  author    = {S. Li},
  title     = {Phylogenetic tree construction using {M}arkov chain {M}onte {C}arlo},
  school    = {Ohio State University},
  year      = 1996,
}

@Article{li90,
  author    = {W. H. Li and M. Gouy and P. M. Sharp and C. O'Huigin and Y.-W. Yang},
  title     = {Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla, and carnivora and molecular clocks},
  journal   = {Proceedings of the National Academy of Sciences, U.S.A.},
  year      = 1990,
  volume    = 87,
  pages     = {6703--6707}
}

@Article{leitner97,
  author    = {T. Leitner and S. Kumar and J. Albert},
  title     = {Tempo and mode of nucleotide substitutions in {\it gag} and {\it env} gene fragments in human immunodeficiency virus type 1 populations with a known transmission history},
  journal   = {Journal of Virology},
  year      = 1997,
  volume    = 71,
  pages     = {4761--4770}
}

@Book{linnaeus58,
  author    = {C. Linnaeus},
  title     = {Systema naturae. {R}egnum animale},
  publisher = {British Museum},
  year      = 1758,
  address   = {London}
}

@article{liu07,
author = {Liu, Liang and Pearl, Dennis K},
title = {{Species trees from gene trees: reconstructing {B}ayesian posterior distributions of a species phylogeny using estimated gene tree distributions}},
journal = {Syst. Biol.},
year = {2007},
volume = {56},
number = {3},
pages = {504--514}
}

@Article{lunn00,
  author    = {D. J. Lunn and A. Thomas and N. Best and D. Spiegelhalter},
  title     = {Win{BUGS} --- a {B}ayesian modelling framework: concepts, structure, and extensibility},
  journal   = {Statistics and Computing},
  year      = 2000,
  volume    = 10,
  pages     = {325--337}
}

@InCollection{lunter04,
  author    = {G. A. Lunter and A. J. Drummond and I. Mikl\'{o}s and J. Hein},
  editor    = {R. Nielsen},
  booktitle = {Statistical methods in Molecular Evolution},
  title     = {Statistical Alignment: Recent Progress, New Applications, and Challenges},
  publisher = {Springer Verlag},
  series    = {Series in Statistics in Health and Medicine},
  year      = 2004
}

@Article{losos98,
  author    = {J. B. Losos and T. R. Jackman and A. Larson and D. de Queiroz and L. Rodr\'iguez-Schettino},
  title     = {Contingency and determinism in replicated adaptive radiations of island lizards},
  journal   = {Science},
  year      = 1998,
  volume    = 279,
  pages     = {2115--2118}
}

@Article{lunter07,
  Author    = "G. A. Lunter",
  Title     = "{{H}{M}{M}o{C}--a compiler for hidden {M}arkov models}",
  Journal   = "Bioinformatics",
  Year      = "2007",
  Volume    = "23",
  Number    = "18",
  Pages     = "2485--2487",
  Month     = "Sep"
}

@Article{luo07,
  author    = {R. Luo and A. L. Hipp and B. Larget},
  title     = {A {B}ayesian model of {AFLP} marker evolution and phylogenetic inference},
  journal   = {Statistical Applications in Genetics and Molecular Biology},
  year      = 2007,
  volume    = 6,
  pages     = {1}
}

@Article{luo08,
  author    = {R. Luo and B. Larget},
  title     = {Modeling substitution and indel processes for {AFLP} marker evolution and phylogenetic inference},
  journal   = {The Annals of Applied Statistics},
  year      = "In Press",
  volume    = [],
  pages     = {[]--[]}
}

@Article{lutzoni00,
  author    = {F. Lutzoni and P. Wagner and V. Reeb and S. Zoller},
  title     = {Integrating ambiguously aligned regions of {DNA} sequences in phylogenetic analysis without violating positional homology},
  journal   = {Systematic Biology},
  year      = 2000,
  volume    = 49,
  pages     = {628--651}
}

%*********************************************************************************
% M
%*********************************************************************************

@Article{maeta98,
  author    = {Y. Maeta and K. Takahashi and N. Shimada},
  title     = {Host body size as a factor determining the egg complement of {S}trepsiptera, an insect parasite},
  journal   = {International Journal of Insect Morphology and Embryology},
  year      = 1998,
  volume    = 27,
  pages     = {27--37}
}

@Article{maddison91,
  author    = {D. R. Maddison},
  title     = {The discovery and importance of multiple islands of most-parsimonious trees},
  journal   = {Systematic Zoology},
  year      = 1991,
  volume    = 40,
  pages     = {315--328}
}

@Article{maddison89,
  author    = {W. P. Maddison},
  title     = {Reconstructing character evolution on polytomous cladograms},
  journal   = {Cladistics},
  year      = 1989,
  volume    = 5,
  pages     = {365--377}
}

@Article{maddison92,
  author    = {D. R. Maddison and M. Ruvolo and D. L. Swofford},
  title     = {Geographic origins of human mitochondrial {DNA} phylogenetic inference from control region sequences},
  journal   = {Systematic Biology},
  year      = 1992,
  volume    = 41,
  pages     = {111--124}
}

@Article{maddison97,
  author    = {W. P. Maddison},
  title     = {Gene trees in species trees},
  journal   = {Systematic Biology},
  year      = 1997,
  volume    = 46,
  pages     = {523--536}
}

@Article{maddison06,
  author    = {W. P. Maddison and D. R. Maddison},
  title     = {Mesquite: a modular system for evolutionary analysis, {V}ersion 1.12},
  journal   = {http://mesquiteproject.org},
  year      = 2006
}

@Article{maguire52,
  author    = {B. A. Maguire and E. S. Pearson and A. H. A. Wynn},
  title     = {The time intervals between industrial accidents},
  journal   = {Biometrika},
  year      = 1952,
  volume    = 39,
  pages     = {168--180}
}

@Book{malecot48,
  author    = {G. Mal\'ecot},
  title     = {Les {M}ath\'ematiques Dt {H}\'er\'edit\'e},
  publisher = {Masson et Cie},
  year      = 1948,
  address   = {Paris}
}

@Article{marshall06,
  author    = {D. C. Marshall and C. Simon and T. R. Buckley},
  title     = {Accurate branch length estimation in partitioned {B}ayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors},
  journal   = {Systematic Biology},
  year      = 2006,
  volume    = 55,
  pages     = {993--1003}
}

@InProceedings{matsuda96,
  author    = {H. Matsuda},
  editor    = {L. Hunter and T. E. Klein},
  title     = {Protein phylogenetic inference using maximum likelihood with a genetic algorithm},
  booktitle = {Pacific {S}ymposium on {B}iocomputing},
  publisher = {World Scientific},
  year      = 1996,
  pages     = {512--523}
}

@Article{mathews99,
  author    = {D. H. Mathews and J. Sabina and M. Zuker and D. H. Turner},
  title     = {Expanded sequence dependence of thermodynamic parameters improves prediction of {RNA} secondary structure},
  journal   = {Journal of Molecular Biology},
  year      = 1999,
  volume    = 288,
  pages     = {911--940}
}

@Article{mathews02,
  author    = {D. H. Mathews and D. H. Turner},
  title     = {Dynalign: an algorithm for finding the secondary structure common to two RNA sequences},
  journal   = {Journal of Molecular Biology},
  year      = 2002,
  volume    = 317,
  pages     = {191--203}
}

@Article{mathews06,
  author    = {D. H. Mathews and D. H. Turner},
  title     = {Prediction of {RNA} secondary structure by free energy minimization},
  journal   = {Current Opinion in Structural Biology},
  year      = 2006,
  volume    = 16,
  pages     = {270--278}
}

@Phdthesis{mau96,
  author    = {B. Mau},
  title     = {Bayesian phylogenetic inference via {M}arkov chain {M}onte {C}arlo methods},
  school    = {University of Wisconsin},
  year      = 1996,
}

@Article{mau97,
  author    = {B. Mau and M. A. Newton},
  title     = {Phylogenetic inference for binary data on dendograms using {M}arkov chain {M}onte {C}arlo},
  journal   = {Journal of Computational and Graphical Statistics},
  year      = 1997,
  volume    = 6,
  pages     = {122--131}
}

@Article{mau99,
  author    = {B. Mau and M. A. Newton and B. Larget},
  title     = {Bayesian phylogenetic inference via {M}arkov chain {M}onte {C}arlo methods},
  journal   = {Biometrics},
  year      = 1999,
  volume    = 55,
  pages     = {1--12}
}

@Article{mcguire07,
  author    = {J. A. McGuire and C. C. Witt and D. L. Altshuler and J. V. Remsen},
  title     = {Phylogenetic systematics and biogeography of hummingbirds: {B}ayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy},
  journal   = {Systematic Biology},
  year      = 2007,
  volume    = 56,
  pages     = {837--856}
}

@Article{mckeown92,
  author    = {M. McKeown},
  title     = {Alternative m{RNA} splicing},
  journal   = {Annual Review of Cell Biology},
  year      = 1992,
  volume    = 8,
  pages     = {133--155}
}

@Article{melefors93,
  author    = {O. Melefors and M. W. Hentze},
  title     = {Translational regulation by m{RNA}/protein interactions in eukaryotic cells: ferritin and beyond},
  journal   = {BioEssays},
  year      = 1993,
  volume    = 15,
  pages     = {85--90}
}

@Article{messier97,
  author    = {W. Messier and C. B. Stewart},
  title     = {Episodic adaptive evolution of primate lysozymes},
  journal   = {Nature},
  year      = 1997,
  volume    = 385,
  pages     = {151--154}
}

@Article{metropolis53,
  author    = {N. Metropolis and A. W. Rosenbluth and M. N. Rosenbluth and A. H. Teller and E. Teller},
  title     = {Equation of state calculations by fast computing machines},
  journal   = {Journal of Chemical Physics},
  year      = 1953,
  volume    = 21,
  pages     = {1087--1092}
}

@Article{metzker02,
  author    = {M. L. Metzker and D. P. Mindell and X. M. Liu and R. G. Ptak and R. A. Gibbs and D. M. Hillis},
  title     = {Molecular evidence of {HIV}-1 transmission in a criminal case},
  journal   = {Proceedings of the National Academy of Sciences, U. S. A.},
  year      = 2002,
  volume    = 99,
  pages     = {14292--14297}
}

@Article{meyer04,
  author    = "I. M. Meyer and R. Durbin",
  title     = "Gene structure conservation aids similarity based gene prediction",
  journal   = NAR,
  year      = 2004,
  volume    = 32,
  number    = 2,
  pages     = "776--783"
}

@Article{michel00,
  author    = {F. Michel and M. Costa and I. Massire and E. Westhof},
  title     = {Modeling {RNA} tertiary structure from patterns of sequence variation},
  journal   = {Methods Enzymology},
  year      = 2000,
  volume    = 317,
  pages     = {491--510}
}

@article{miller88,
  author    = {W. Miller and E. W. Myers},
  title     = {Sequence comparison with concave weighting functions},
  journal   = BMB,
  year      = 1988,
  volume    = 50,
  pages     = {97--120}
}

@article{minin07,
  author    = {V. N. Minin and M. A. Suchard},
  title     = {Counting labeled transitions in continuous-time Markov models of evolution},
  journal   = {Journal of Mathematical Biology},
  year      = {In Press}
}

@article{miklos04,
  author    = {I. Mikl\'{o}s and G. Lunter and I. Holmes},
  title     = {A long indel model for evolutionary sequence alignment},
  journal   = MBE,
  year      = 2004,
  volume    = 21,
  number    = 3,
  pages     = {529--540}
}

@article{mitchison99,
  author    = {G. J. Mitchison},
  title     = {A probabilistic treatment of phylogeny and sequence alignment},
  journal   = JME,
  year      = 1999,
  volume    = 49,
  number    = 1,
  pages     = {11-22}
}

@Article{miyake71,
  author    = {T. Miyake and I. Haruna and T. Shiba and Y. H. Itoh and K. Yamane and I. Watanabe},
  title     = {Grouping of {RNA} phages based on template specificity of their {RNA} replicases},
  journal   = {Proceedings of the National Academy of Sciences, USA},
  year      = 1971,
  volume    = 68,
  pages     = {2022--2024}
}

@Article{miyamoto85,
  author    = {M. M. Miyamoto},
  title     = {Consensus cladograms and general classifications},
  journal   = {Cladistics},
  year      = 1985,
  volume    = 1,
  pages     = {186--189}
}

@Article{miyata80,
  author    = {T. Miyata and T. Yasunaga},
  title     = {Molecular evolution of m{RNA}: {A} method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application},
  journal   = {Journal of Molecular Evolution},
  year      = 1980,
  volume    = 16,
  pages     = {23--36}
}

@Article{mohri00,
  author    = {M. Mohri and F. Pereira and M. Riley},
  title     = {Weighted Finite-State Transducers in Speech Recognition},
  journal   = {ISCA ITRW Automatic Speech Recognition},
  year      = 2000,
  pages     = {97--106}
}

@Article{moler78,
  author    = {C. Moler and C. Van Loan},
  title     = {Nineteen dubious ways to compute the exponential of a matrix},
  journal   = {SIAM Review},
  year      = 1978,
  volume    = 20,
  pages     = {801--836}
}

@Article{morgenstern99,
  author    = {B. Morgenstern},
  title     = {{DIALIGN} 2: {i}mprovement of the segment-to-segment approach to multiple sequence alignment},
  journal   = {Bioinformatics},
  year      = 1999,
  volume    = 15,
  pages     = {211--218}
}

@Article{morrison97,
  author    = {D. A. Morrison and J. T. Ellis},
  title     = {Effects of nucleotide sequence alignment on phylogeny estimation: {A} case study of {18S} {rDNAs} of {\it {A}picomplexa}},
  journal   = {Molecular Biology and Evolution},
  year      = 1997,
  volume    = 14,
  pages     = {428--441}
}

@Article{moyle06,
  author    = {R. G. Moyle and J. Cracraft and M. Laim and J. Nais and F. H. Sheldon},
  title     = {Reconsideration of the phylogenetic relationships of the enigmatic {B}ornean {B}ristlehead ({\it {P}ityriasis gymnocephala)}},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 2006,
  volume    = 39,
  pages     = {893--898}
}

@Article{mugridge00,
  author    = {N. B. Mugridge and D. A. Morrison and T. Jakel and A. R. Heckeroth and A. M. Tenter and A. M. Johnson},
  title     = {Effects of sequence alignment and structural domains of ribosomal {DNA} on phylogeny reconstruction for the {P}rotozoan family {S}arcocystidae},
  journal   = {Molecular Biology and Evolution},
  year      = 2000,
  volume    = 17,
  pages     = {1842--1853}
}

@Article{muller00,
  author    = {T. Muller and M. Vingron},
  title     = {Modeling amino acid replacement},
  journal   = {Journal of Computational Biology},
  year      = 2000,
  volume    = 7,
  pages     = {761--776}
}

@Article{munch08,
  author    = {K. Munch and W. Boomsmsa and J. P. Huelsenbeck and E. Willerslev and R. Nielsen},
  title     = {Statistical assignment of environmental {DNA} sequence},
  journal   = {Systematic Biology},
  year      = 2008,
  volume    = 57,
  pages     = {750--757}
}

@Article{murphy01,
  author    = {W. J. Murphy and E. Eizirik and S. J. O'Brien and O. Madsen and M. Scally and C. Douady and
               E. Teeling and O. A. Ryder and M. Stanhope and W. W. De Jong and M. S. Springer},
  title     = {Resolution of the early placental mammal radiation using {B}ayesian phylogenetics},
  journal   = {Science},
  year      = 2001,
  volume    = 294,
  pages     = {2348--2351}
}

@Article{muse94,
  author    = {S. V. Muse and B. S. Gaut},
  title     = {A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome},
  journal   = {Molecular Biology and Evolution},
  year      = 1994,
  volume    = 11,
  pages     = {715--724}
}

%*********************************************************************************
% N
%*********************************************************************************

@Article{navidi91,
  author    = {W. C. Navidi and G. A. Churchill and A. von Haeseler},
  title     = {Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants},
  journal   = {Molecular Biology and Evolution},
  year      = 1991,
  volume    = 8,
  pages     = {128--143}
}

@Article{neal00,
  author    = {R. M. Neal},
  title     = {Markov chain sampling methods for {D}irichlet process mixture models},
  journal   = {Journal of Computational and Graphical Statistics},
  year      = 2000,
  volume    = 9,
  pages     = {249--265}
}

@Article{nee94,
  author    = {S. Nee and R. M. May and P. H. Harvey},
  title     = {The reconstructed evolutionary process},
  journal   = {Philosophical Transactions of the Royal Society of London B},
  year      = 1994,
  volume    = 344,
  pages     = {305--311}
}

@Article{needleman70,
  author    = 	 "S. B. Needleman and C. D. Wunsch",
  title     = 	 "A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins",
  journal   = 	 JMB,
  year      = 	 1970,
  volume    = 	 48,
  pages     = 	 "443--453"
}

@InProceedings{nei91,
  author    = {M. Nei},
  editor    = {M. M. Miyamoto and J. Cracraft},
  title     = {Relative efficiencies of different tree-making methods for molecular data},
  booktitle = {Phylogenetic {A}nalysis of {DNA} {S}equences},
  publisher = {Oxford University Press},
  year      = 1991,
  pages     = {90--128}
}

@Article{nei83,
  author    = {M. Nei and F. Tajima and Y. Tateno},
  title     = {Accuracy of estimated phylogenetic trees from molecular data. {II}. {G}ene frequency data},
  journal   = {Journal of Molecular Evolution},
  year      = 1983,
  volume    = 19,
  pages     = {153--170}
}

@Article{nei86,
  author    = {M. Nei and T. Gojobori},
  title     = {Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions},
  journal   = {Molecular Biology and Evolution},
  year      = 1986,
  volume    = 3,
  pages     = {418--426}
}

@Article{nielsen97,
  author    = {R. Nielsen},
  title     = {Site-by-site estimation of the rate of evolution and the correlation of rates in mitochondrial {DNA}},
  journal   = {Systematic Biology},
  year      = 1997,
  volume    = 46,
  pages     = {346--353}
}

@Article{nielsen98,
  author    = {R. Nielsen and Z. Yang},
  title     = {Likelihood models for detecting positively selected amino acid sites and applications to the {HIV-1} envelope gene},
  journal   = {Genetics},
  year      = 1998,
  volume    = 148,
  pages     = {929--93}
}

@Article{nielsen02,
  author    = {R. Nielsen},
  title     = {Mapping mutations on phylogenies},
  journal   = {Systematic Biology},
  year      = 2002,
  volume    = 51,
  pages     = {729--739}
}

@Article{newton94,
  author    = {M. A. Newton and A. E. Raftery},
  title     = {Approximate {B}ayesian inference by the weighted likelihood bootstrap},
  journal   = {Journal of the Royal Statistical Society, B},
  year      = 1994,
  volume    = 56,
  pages     = {3--48}
}

@InProceedings{newton99,
  author    = {M. Newton and B. Mau and B. Larget},
  editor    = {F. Seillier-Moseiwitch},
  title     = {Markov chain {M}onte {C}arlo for the {B}ayesian analysis of evolutionary trees from aligned molecular sequences},
  booktitle = {Statistics in {M}olecular {B}iology and {G}enetics},
  publisher = {IMS Lecture Notes-Monograph Series, Volume 33},
  year      = 1999,
  pages     = {143--162}
}

@Article{neyman48,
  author    = {J. Neyman and E. L. Scott},
  title     = {Consistent estimates based on partially consistent observations},
  journal   = {Econometrica},
  year      = 1948,
  volume    = 16,
  pages     = {1--32}
}

@InProceedings{neyman71,
  author    = {J. Neyman},
  editor    = {S. S. Gupta and J. Yackel},
  title     = {Molecular studies of evolution: {A} source of novel statistical problems},
  booktitle = {Statistical Decision Theory and Related Topics},
  publisher = {Academic Press},
  year      = 1971,
  pages     = {1--27}
}

@Article{notredame00,
  author    = {C. Notredame and D. G. Higgins and J. Heringa},
  title     = {T-Coffee: A novel method for fast and accurate multiple sequence alignment},
  journal   = {Journal of Molecular Biology},
  year      = 2000,
  volume    = 302,
  pages     = {205--217}
}

@Article{nylander04,
  author    = {J. A. A. Nylander and F. Ronquist and J. P. Huelsenbeck and J. L. Nieves Aldrey},
  title     = {Bayesian phylogenetic analysis of combined data},
  journal   = {Systematic Biology},
  year      = 2004,
  volume    = 53,
  pages     = {47--67}
}

%*********************************************************************************
% O
%*********************************************************************************

@Article{odonell59,
  author    = {C. A. O'Donell},
  title     = {Convolvulaceas argentinas},
  journal   = {Lilloa},
  year      = 1959,
  volume    = 29,
  pages     = {87--343}
}

@Article{ooyen79,
  author    = {A. van Ooyen and J. van den Berg and N. Mantel and C. Weissmann},
  title     = {Comparison of total sequence of a cloned rabbit $\beta$-globin gene and its flanking regions with a homologous mouse sequence},
  journal   = {Science},
  year      = 1979,
  volume    = 206,
  pages     = {337--344}
}

@Article{otha93,
  author    = {T. Otha},
  title     = {Pattern of nucleotide substitutions in growth hormone-{P}rolactin gene family: {A} paradigm for evolution by gene duplication},
  journal   = {Genetics},
  year      = 1993,
  volume    = 134,
  pages     = {1271--1276}
}

@Article{ou92,
  author    = {C. -Y. Ou and C. A. Ciesielski and G. Myers and C. I. Bandea and C. -C. Luo and B. T. M. Korber and J. I. Mullins and G. Schochetman and
              R. L. Berkelman and A. N. Economou and J. J. Witte and L. J. Furman and G. A. Satten and K. A. MacInnes and J. W. Curran and H. W. Jaffe},
  title     = {Molecular epidemiology of {HIV} transmission in a dental practice},
  journal   = {Science},
  year      = 1992,
  volume    = 256,
  pages     = {1165-1171}
}

@Book{owen43,
  author    = {R. Owen},
  title     = {Lectures on the {C}omparative {A}natomy and {P}hysiology of the {I}nvertebrate {A}nimals, delivered at the {R}oyal {C}ollege of {S}urgeons},
  publisher = {Longman, Brown, Green, and Longmans},
  year      = 1843,
  address   = {London}
}

%*********************************************************************************
% P
%*********************************************************************************

@Article{page01,
  author    = {S. L. Page and M. Goodman},
  title     = {Catarrhine phylogeny: noncoding {DNA} evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 2001,
  volume    = 18,
  pages     = {14--25}
}

@Article{pagel99,
  author    = {M. Pagel},
  title     = {The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies},
  journal   = {Systematic Biology},
  year      = 1999,
  volume    = 48,
  pages     = {612--622}
}

@Article{pagel04,
  author    = {M. Pagel and A. Meade},
  title     = {A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data},
  journal   = {Systematic Biology},
  year      = 2004,
  volume    = 53,
  pages     = {571--581}
}
@InProceedings{pagel05,
  author    = {M. Pagel and A. Meade},
  editor    = {O. Gascuel},
  title     = {Mixture models in phylogenetic inference},
  booktitle = {Mathematics of Evolution and Phylogeny},
  publisher = {Oxford University Press},
  year      = 2005,
  pages     = {121--142}
}


@Article{palumbi89,
  author    = {S. R. Palumbi},
  title     = {Rates of molecular evolution and the function of nucleotide positions free to vary},
  journal   = {Journal of Molecular Evolution},
  year      = 1989,
  volume    = 29,
  pages     = {180--187}
}

@Article{pamilo88,
  author    = {P. Pamilo and M. Nei},
  title     = {Relationships between gene trees and species trees},
  journal   = {Molecular Biology and Evolution},
  year      = 1988,
  volume    = 5,
  pages     = {568--583}
}

@Article{pamilo93,
  author    = {P. Pamilo and N. O. Bianchi},
  title     = {Evolution of the {Z}fx and {Z}fv genes: {R}ates and interdependence between the genes},
  journal   = {Molecular Biology and Evolution},
  year      = 1993,
  volume    = 10,
  pages     = {271--281}
}

@Article{patterson88,
  author    = {C. Patterson},
  title     = {Homology in classical and molecular biology},
  journal   = {Molecular Biology and Evolution},
  year      = 1988,
  volume    = 5,
  pages     = {603--625}
}

@Article{peacock75,
  author    = {D. Peacock and D. Boulter},
  title     = {Use of amino acid sequence data in phylogeny and evaluation of methods using computer simulation},
  journal   = {Journal of Molecular Biology},
  year      = 1975,
  volume    = 95,
  pages     = {513--527}
}

@Article{pella06,
  author    = {J. Pella and M. Masuda},
  title     = {The {G}ibbs and split-merge sampler for population mixture analysis from genetic data with incomplete baselines},
  journal   = {Can. J. Fish. Aquat. Sci.},
  year      = 2006,
  volume    = 63,
  pages     = {576--596}
}

@Article{peltz92,
  author    = {S. W. Peltz and A. Jacobson},
  title     = {m{RNA} stability: in trans-it},
  journal   = {Current Opinion in Cell Biology},
  year      = 1992,
  volume    = 4,
  pages     = {979--983}
}

@Article{pettigrew86,
  author    = {J. D. Pettigrew},
  title     = {Flying primates? {M}egabats have the advanced pathway from eye to midbrain},
  journal   = {Science},
  year      = 1986,
  volume    = 231,
  pages     = {1304--1306}
}

@Article{pettigrew91a,
  author    = {J. D. Pettigrew},
  title     = {Wings or brain? {C}onvergent evolution in the origin of bats},
  journal   = {Systematic Zoology},
  year      = 1991,
  volume    = 40,
  pages     = {199--216}
}

@Article{pettigrew91b,
  author    = {J. D. Pettigrew},
  title     = {A fruitful wrong hypothesis? {R}esponse to {B}aker, {N}ovacek, and {S}immons},
  journal   = {Systematic Zoology},
  year      = 1991,
  volume    = 40,
  pages     = {231--239}
}

@Article{pettigrew94,
  author    = {J. D. Pettigrew},
  title     = {Flying {DNA}},
  journal   = {Systematic Zoology},
  year      = 1994,
  volume    = 40,
  pages     = {277--280}
}

@Article{pitman02,
  author    = {J. Pitman},
  title     = {Combinatorial stochastic processes},
  journal   = {Technical Report 621, University of California at Berkeley, lecture notes for St. Flour Summer School},
  year      = 2002
}

@Article{plaisant02,
  author    = {C. Plaisant and J. Grosjean and B. B. Bederson},
  title     = {{SpaceTree}: {S}upporting exploration in large node link tree, design evolution and empirical evaluation},
  journal   = {Proceedings of the Information Visualization Symposium},
  year      = 2002,
  pages     = {57--64}
}

@Article{pond04,
  author    = {S. L. Kosakovsky Pond and S. V. Muse},
  title     = {Column sorting: {R}apid calculation of the phylogenetic likelihood},
  journal   = {Systematic Biology},
  year      = 2004,
  volume    = 50,
  pages     = {685--692}
}

@Book{popper59,
  author    = {K. R. Popper},
  title     = {The {L}ogic of {S}cientific {D}iscovery},
  publisher = {Basic Books},
  year      = 1959,
  address   = {New York}
}

@Book{popper83,
  author    = {K. R. Popper},
  title     = {Realism and the {A}im of {S}cience. [{V}ol. 1. of the {P}ostscript to {T}he {L}ogic of {S}cientific {D}iscovery]},
  publisher = {Routledge},
  year      = 1983,
  address   = {London}
}

@Article{poux08,
  author    = {C. Poux and O. Madsen and J. Glos and W. W. de Jong and M. Vences},
  title     = {Molecular phylogeny and divergence times of {M}alagasy tenrecs: {I}nfluence of data partitioning and taxon sampling on dating analyses},
  journal   = {BMC Evolutionary Biology},
  year      = 2008,
  volume    = 8,
  pages     = {102}
}

@Book{press92,
  author    = {W. H. Press and S. A. Teukolsky and W. T. Vetterling and B. P. Flannery},
  title     = {Numerical {R}ecipes in {C}},
  publisher = {Cambridge University Press},
  year      = 1992,
  address   = {Cambridge}
}

@InProceedings{patterson82,
  author    = {C. Patterson},
  editor    = {K. A. Joysey and A. B. Friday},
  title     = {Morphological Characters and Homology},
  booktitle = {Problems of {P}hylogenetic {R}econstruction},
  publisher = {Academic Press},
  year      = 1982,
  pages     = {21-74}
}

@Article{pritchard00,
  author    = {J. K. Pritchard and M. Stephens and P. Donnelly},
  title     = {Inference of population structure using multilocus genotype data},
  journal   = {Genetics},
  year      = 2000,
  volume    = 155,
  pages     = {945--959}
}

@article{posada98,
author = "David Posada",
title = "Model{T}est: testing the model of {DNA} substitution",
journal = "Bioinformatics",
year = "1998",
volume = "14",
pages = "817--818"
}

@article{posada08,
author = "David Posada", 
journal = "Mol. Biol. Evol.",
title = "j{M}odel{T}est: phylogenetic model averaging",
year = "2008",
volume = "25",
pages = "1253--1256",
}

%*********************************************************************************
% Q
%*********************************************************************************

%*********************************************************************************
% R
%*********************************************************************************

@Article{ragan01,
  author    = {M. Ragan},
  title     = {Detection of lateral gene transfer among microbial genomes},
  journal   = {Curr. Opin. Genet. Dev.},
  year      = 2001,
  volume    = 11,
  pages     = {620--626}
}

@InProceedings{raftery96,
  author    = {A. Raftery},
  editor    = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  title     = {Hypothesis testing and model selection},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  publisher = {Chapman and Hall},
  year      = 1996,
  pages     = {163--187}
}

@Article{rambaut97,
  author    = {A. Rambaut and N. C. Grassly},
  title     = {{Seq-Gen}: an application for the {M}onte {C}arlo simulation of {DNA} sequence evolution along phylogenetic trees},
  journal   = {Computer Applications in the Biosciences},
  year      = 1997,
  volume    = 13,
  pages     = {235--238}
}

@Misc{rambaut07,
  author       = {A. Rambaut and A. J. Drummond},
  title        = {Tracer v1.4},
  howpublished = {http://beast.bio.ed.ac.uk/Tracer},
  year         = 2007
}

@Article{rannala98,
  author    = {B. Rannala and J. P. Huelsenbeck and Z. Yang and R. Nielsen},
  title     = {Taxon sampling and the accuracy of large phylogenies},
  journal   = {Systematic Biology},
  year      = 1998,
  volume    = 47,
  pages     = {702--719}
}

@Article{rannala96,
  author    = {B. Rannala and Z. Yang},
  title     = {Probability distribution of molecular evolutionary trees: {A} new method of phylogenetic inference},
  journal   = {Journal of Molecular Evolution},
  year      = 1996,
  volume    = 43,
  pages     = {304--311}
}

@Article{rannala07,
  author    = {B. Rannala and Z. Yang},
  title     = {Inferring speciation times under an episodic molecular clock},
  journal   = {Systematic Biology},
  year      = 2007,
  volume    = 56,
  pages     = {453--466}
}

@Article{raup74,
  author    = {D. M. Raup and S. J. Gould},
  title     = {Stochastic simulation and evolution of morphology---towards a nomothetic paleontology},
  journal   = {Systematic Zoology},
  year      = 1974,
  volume    = 23,
  pages     = {305--322}
}

@Article{raup73,
  author    = {D. M. Raup and S. J. Gould and T. J. M. Schopf and D. S. Simberloff},
  title     = {Stochastic models of phylogeny and the evolution of diversity},
  journal   = {Journal of Geology},
  year      = 1973,
  volume    = 81,
  pages     = {525--542}
}

@Article{redelings05,
  author    = {B. D. Redelings and M. A. Suchard},
  title     = {Joint Bayesian estimation of alignment and phylogeny},
  journal   = {Systematic Biology},
  year      = 2005,
  volume    = 54,
  pages     = {401--418}
}

@Article{redelings07,
  author    = {B. D. Redelings and M. A. Suchard},
  title     = {Incorporating indel information into phylogeny estimation for rapidly emerging pathogens},
  journal   = {BMC Evolutionary Biology},
  year      = 2007,
  volume    = 7,
  pages     = {40}
}

@Article{ribeiro98,
  author    = {S. Ribeiro and G. B. Golding},
  title     = {The mosaic nature of the eukayote nucleus},
  journal   = {Molecular Biology and Evolution},
  year      = 1998,
  volume    = 7,
  pages     = {779--788}
}

@Book{rice95,
  author    = {J. A. Rice},
  title     = {Mathematical {S}tatistics and {D}ata {A}nalysis},
  publisher = {Duxbury Press},
  year      = 1995,
  address   = {Belmont, California}
}

@Article{ritland87,
  author    = {K. Ritland and M. T. Clegg},
  title     = {Evolutionary analysis of plant {DNA} sequences},
  journal   = {American Naturalist},
  year      = 1987,
  volume    = 130,
  pages     = {S74--S100}
}

@Article{robbins18,
  author    = {R. B. Robbins},
  title     = {Some applications of mathematics to breeding problems, {II}},
  journal   = {Genetics},
  year      = 1918,
  volume    = 3,
  pages     = {73--92}
}

@InProceedings{robinson79,
  author    = {D. F. Robinson and L. R. Foulds},
  editor    = {A. F. Horadam and W. D. Wallis},
  title     = {Comparison of weighted labelled trees},
  booktitle = {Combinatorial Mathematics VI. Proceedings of the Sixth Australian Conference on Combinatorial Mathematics, Armidale, Australia, August 1978},
  publisher = {Springer-Verlag},
  year      = 1979,
  pages     = {119--126}
}

@Article{robinson81,
  author    = {D. F. Robinson and L. R. Foulds},
  title     = {Comparison of phylogenetic trees},
  journal   = {Mathematical Biosciences},
  year      = 1981,
  volume    = 53,
  pages     = {131--147}
}

@Article{robinson03,
  author    = {D. M. Robinson and D. T. Jones and H. Kishino and N. Goldman and J. L. Thorne},
  title     = {Protein evolution with dependence among codons due to tertiary structure},
  journal   = {Molecular Biology and Evolution},
  year      = 2003,
  volume    = 20,
  pages     = {1692--1704}
}

@Article{rodrigue05,
  author    = {N. Rodrigue and N. Lartillot and D. Bryant and H. Philippe},
  title     = {Site interdependence attributed to tertiary structure in amino acid sequence evolution},
  journal   = {Gene},
  year      = 2005,
  volume    = 347,
  pages     = {207--217}
}

@Article{rodrigue08,
  author    = {N. Rodrigue and H. Philippe and N. Lartillot},
  title     = {Uniformization for sampling realizations of {M}arkov processes: {A}pplications to {B}ayesian implementations of codon substitution models},
  journal   = {Bioinformatics},
  year      = 2008,
  volume    = 24,
  pages     = {56--62}
}

@Article{rodriguez90,
  author    = {F. Rodriguez and J. F. Oliver and A. Marin and J. R. Medina},
  title     = {The general stochastic model of nucleotide substitutions},
  journal   = {Journal of Theoretical Biology},
  year      = 1990,
  volume    = 142,
  pages     = {485--501}
}

@Article{rogers97,
  author    = {J. S. Rogers},
  title     = {On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences},
  journal   = {Systematic Biology},
  year      = 1997,
  volume    = 46,
  pages     = {354--357}
}

@Article{rogers98,
  author    = {J. S. Rogers and D. L. Swofford},
  title     = {A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences},
  journal   = {Systematic Biology},
  year      = 1998,
  volume    = 47,
  pages     = {77--89}
}

@Article{rohl04,
  author    = {C. A. Rohl and C. E. Strauss and K. M. Misura and D. Baker},
  title     = {Protein structure prediction using {R}osetta},
  journal   = {Methods of Enzymology},
  year      = 2004,
  volume    = 383,
  pages     = {66--93}
}

@Article{ronquist03,
  author    = {F. Ronquist and J. P. Huelsenbeck},
  title     = {MrBayes 3: {B}ayesian phylogenetic inference  under mixed models},
  journal   = {Bioinformatics},
  year      = 2003,
  volume    = 19,
  pages     = {1572--1574}
}

@Article{ronquist04a,
  author    = {F. Ronquist},
  title     = {Bayesian inference of character evolution},
  journal   = {Trends in Ecology and Evolution},
  year      = 2004,
  volume    = 19,
  pages     = {475--481}
}

@InProceedings{ronquist04b,
  author    = {F. Ronquist and J. P. Huelsenbeck and T. Britton},
  editor    = {O. Bininda-Emonds},
  title     = {Bayesian supertrees},
  booktitle = {Phylogenetic supertrees: Combining information to reveal the tree of life, Computational Biology, Volume 4},
  publisher = {Kluwer Academic Publishers, The Netherlands},
  year      = 2004,
  pages     = {193--224}
}


@Article{ronquist06,
  author    = {F. Ronquist and B. Larget and J. P. Huelsenbeck and J. B. Kadane and D. Simon and P. van der Mark},
  title     = {Comment on `{P}hylogenetic {MCMC} algorithms are misleading on mixtures of trees},
  journal   = {Science},
  year      = 2006,
  volume    = 312,
  pages     = {367}
}

@InProceedings{ronquist09,
  author    = {F. Ronquist and P. van der Mark and J. P. Huelsenbeck},
  editor    = {P. Lemey and M. Salemi and A. M. Vandamme},
  title     = {Bayesian analysis of molecular evolution using {MrBayes}},
  booktitle = {The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Second Edition},
  publisher = {Cambridge University Press},
  year      = 2009,
  pages     = {1--1}
}


@article{ronquist10,
    author  = {Fredrik Ronquist and Andrew R. Deans},
    title   = "Bayesian phylogenetic inference and its influence on insect systematics",
    year    = "2010",
    journal = "Annual Review of Entomology",
    volume  = "55",
    pages   = "189--206"
}

@article{ronquist11,
    author  = {Fredrik Ronquist and Maxim Teslenko and Paul van der Mark and Daniel Ayres and
                     Aaron Darling and Sebastian H\"ohna and Bret Larget and Liang Liu and Marc A. Suchard
                     and John P. Huelsenbeck},
    title   = "Mr{B}ayes 3.2: Efficient {B}ayesian phylogenetic inference and model choice across a large model space",
    year    = "2011",
    journal = "Systematic Biology",
    volume  = "in press",
    pages   = "000--000"
}

@article{ronquist12,
    author  = {Fredrik Ronquist and Seraina Klopfstein and Lars Vilhelmsen and Susanne Schulmeister and
                     Debra L. Murray and Alexandr P. Rasnitsyn},
    title   = "A total-evidence approach to dating, applied to the early radiation of Hymenoptera",
    year    = "2012",
    journal = "Systematic Biology",
    volume  = "in press",
    pages   = "000--000"
}

@Article{ross02,
  author    = {H. A. Ross and A. G. Rodrigo},
  title     = {Immune-mediated positive selection drives {H}uman {I}mmunodeficiency {V}irus {T}ype 1 molecular variation and predicts disease duration},
  journal   = {Journal of Virology},
  year      = 2002,
  volume    = 76,
  pages     = {11715--11720}
}

@Article{rougemont07,
  author    = {J. Rougemont and B. Nyffeler and S. E. Antonarakis},
  title     = {Early history of mammals is elucidated with the {ENCODE} multiple species sequencing data},
  journal   = {PLoS Genetics},
  year      = 2007,
  volume    = 3,
  pages     = {e2}
}

@Book{russell16,
  author    = {E. S. Russell},
  title     = {Form and {F}unction},
  publisher = {J. Murray},
  year      = 1916,
  address   = {London}
}

@Article{russell97,
  author    = {R. B. Russell and M. A. Saqi and R. A. Sayle and P. A. Bates and M. J. Sternberg},
  title     = {Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation},
  journal   = {Journal of Molecular Biology},
  year      = 1997,
  volume    = 269,
  pages     = {423--439}
}

@Article{rzhetsky95,
  author    = {A. Rzhetsky},
  title     = {Estimating substitution rates in ribosomal {RNA} genes},
  journal   = {Genetics},
  year      = 1995,
  volume    = 141,
  pages     = {771--783}
}

@Book{robert02,
  author    = {C. P. Robert and G. Casella},
  title     = {Monte {C}arlo {S}tatistical {M}ethods},
  publisher = {Springer},
  year      = 2002,
  address   = {New York}
}

%*********************************************************************************
% S
%*********************************************************************************

@Article{sackin72,
  author    = {M. J. Sackin},
  title     = {``Good'' and ``bad'' phenograms},
  journal   = {Systematic Zoology},
  year      = 1972,
  volume    = 21,
  pages     = {225--226}
}

@Article{saitou87,
  author    = {N. Saitou and M. Nei},
  title     = {The neighbor-joining method: {A} new method for reconstructing phylogenetic trees},
  journal   = {Molecular Biology and Evolution},
  year      = 1987,
  volume    = 4,
  pages     = {406--425}
}

@Article{sanderson00,
  author    = {M. J. Sanderson and M. F. Wojciechowski},
  title     = {Improved bootstrap confidence limits in large-scale phylogenies with an example from {N}eo-{A}stragalus ({L}eguminosae)},
  journal   = {Systematic Biology},
  year      = 2000,
  volume    = 49,
  pages     = {671--685}
}

@Article{santiago02,
  author    = {M. L. Santiago and  C. M. Rodenburg and S. Kamenya and F. Bibollet-Ruche and F. Gao and E. Bailes and S. Meleth and 
               S. Soong and J. M. Kilby and Z. Moldoveanu and B. Fahey and M. N. Muller and A. Ayouba and E. Nerrienet and H. M. McClure and
               J. L. Heeney and A. E. Pusey and D. A. Collins and C. Boesch and R. W. Wrangham and J. Goodall and P. M. Sharp and G. M. Shaw and B. H. Hahn},
  title     = {{SIVcpz} in wild chimpanzees },
  journal   = {Science},
  year      = 2002,
  volume    = 295,
  pages     = {465}
}

@Article{satta00,
  author    = {Y. Satta and J. Klein and N. Takahata},
  title     = {{DNA} archives and our nearest relative: The trichotomy problem revisited},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 2000,
  volume    = 14,
  pages     = {259--275}
}

@Article{savage83,
  author    = {H. M. Savage},
  title     = {The shape of evolution: {S}ystematic tree topology},
  journal   = {Biological Journal of the Linnean Society},
  year      = 1983,
  volume    = 20,
  pages     = {225--244}
}

@Article{savolainen00,
  author    = {V. Savolainen and M. W. Chase and S. B. Hoot and C. M. Morton and D. E. Soltis and C. Bayer and M. F. Fay and A. De Bruijn and S. Sullivan and Q. L. Qiu},
  title     = {Phylogenetics of flowering plants based upon a combined analysis of plastid atpB and rbc{L} gene sequences},
  journal   = {Systematic Biology},
  year      = 2000,
  volume    = 49,
  pages     = {306--362}
}

@Article{schluter95,
  author    = {D. Schluter},
  title     = {Uncertainty in ancient phylogenies},
  journal   = {Nature},
  year      = 1995,
  volume    = 377,
  pages     = {108--109}
}

@Article{schluter97,
  author    = {D. Schluter and T. Price and A. {\O}. Mooers and D. Ludwig},
  title     = {Likelihood of ancestor states in adaptive radiation},
  journal   = {Evolution},
  year      = 1997,
  volume    = 51,
  pages     = {1699--1711}
}

@Article{schoniger94,
  author    = {M. Sch{\"o}niger and A. von Haeseler},
  title     = {A stochastic model and the evolution of autocorrelated DNA sequences},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 1994,
  volume    = 3,
  pages     = {240--247}
}

@Article{schoniger95,
  author    = {M. Sch{\"o}niger and A. von Haeseler},
  title     = {Performance of the maximum likelihood, neighbor joining, and maximum parsimony methods when sequence sites are not independent},
  journal   = {Systematic Biology},
  year      = 1995,
  volume    = 44,
  pages     = {533--547}
}

@Article{schroder70,
  author    = {E. Schr{\"o}der},
  title     = {Vier combinatorische probleme},
  journal   = {Zeitschrift f{\"u}r Mathematik und Physik},
  year      = 1870,
  volume    = 15,
  pages     = {361--376}
}

@Article{schultz99,
  author    = {T. R. Schultz and G. A. Churchill},
  title     = {The role of subjectivity in reconstructing ancestral character states: {A} {B}ayesian approach to unknown rates, states, and transformation asymmetries},
  journal   = {Systematic Biology},
  year      = 1999,
  volume    = 48,
  pages     = {651--664}
}

@Article{schwartz06,
  author    = {A. S. Schwartz and E. W. Myers and L. Pachter},
  title     = {Alignment metric accuracy},
  journal   = {http://arxiv.org/abs/q-bio.QM/0510052},
  year      = {Submitted}
}

@Article{schwartz07,
  author    = {A. S. Schwartz and L. Pachter},
  title     = {Multiple alignment by sequence annealingThe evolution of dinosaurs},
  journal   = {Bioinformatics},
  year      = 2007,
  volume    = 23,
  pages     = {e24--e29}
}

@Article{sereno99,
  author    = {P. C. Sereno},
  title     = {The evolution of dinosaurs},
  journal   = {Science},
  year      = 1999,
  volume    = 284,
  pages     = {2137--2147}
}

@Article{shankarappa99,
  author    = {R. Shankarappa and R. B. Margolick and S. J. Gange and A. G. Rodrigo and D. Upchurch and H. Farzadegan and P. Gupta and C. R. Rinaldoand G. H. Learn and X. He and X. L. Huang and J. I. Mullins},
  title     = {Consistent viral evolutionary changes associated with progression of {HIV-1} infection},
  journal   = {Journal of Virology},
  year      = 1999,
  volume    = 73,
  pages     = {10489--10502}
}

@Article{sharp01,
  author    = {P. M. Sharp and E. Bailes and R. R. Chaudhuri and C. M. Rodenburg and M. O. Santiago and B. H. Hahn},
  title     = {The origins of acquired immune deficiency syndrome viruses: {W}here and when?},
  journal   = {Philosophical Transactions of the Royal Society of London, B},
  year      = 2001,
  volume    = 356,
  pages     = {867--876}
}

@Article{shao90,
  author    = {K. T. Shao and R. R. Sokal},
  title     = {Tree balance},
  journal   = {Systematic Zoology},
  year      = 1990,
  volume    = 39,
  pages     = {266--276}
}

@InProceedings{shapiro75,
  author    = {L. Shapiro and I. Bendis},
  editor    = {N. D. Zinder},
  title     = {{RNA} phages of bacteria other than {E}. coli},
  booktitle = {{RNA} {P}hages},
  publisher = {Cold Spring Harbor Laboratory},
  year      = 1975,
  pages     = {397--410}
}

@Article{siddall97,
  author    = {M. E. Siddall and A. G. Kluge},
  title     = {Probabilism and phylogenetic inference},
  journal   = {Cladistics},
  year      = 1997,
  volume    = 13,
  pages     = {313--336}
}

@Article{sierwald01,
  author    = {P. Sierwald and W. A. Shear and R. M. Shelley and J. E. Bond},
  title     = {Millipede phylogeny revisited in the light of the enigmatic order {S}iphoniulida},
  journal   = {Journal of Zoological Systematics and Evolutionary Research},
  year      = 2001,
  volume    = 41,
  pages     = {87--99}
}

@Article{sinsheimer03,
  author    = {J. S.  Sinsheimer and M. A. Suchard and K. S. Dorman and F. Fang and R. E. Weiss},
  title     = {Are you my mother? {B}ayesian phylogenetic inference of recombination among putative parental strains},
  journal   = {Applied Bioinformatics},
  year      = 2003,
  volume    = 2,
  pages     = {131--144}
}

@Article{slatkin91,
  author    = {M. Slatkin and R. R. Hudson},
  title     = {Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations},
  journal   = {Genetics},
  year      = 1991,
  volume    = 129,
  pages     = {555--562}
}

@Article{slatkin97a,
  author    = {M. Slatkin and B. Rannala},
  title     = {Estimating the age of alleles by use of intraallelic variability},
  journal   = {American Journal of Human Genetics},
  year      = 1997,
  volume    = 60,
  pages     = {447--458}
}

@Article{slatkin97b,
  author    = {M. Slatkin and B. Rannala},
  title     = {The sampling distribution of disease-associated alleles},
  journal   = {Genetics},
  year      = 1997,
  volume    = 147,
  pages     = {1855--1861}
}

@article{smith81,
  author    = "B. J. Smith and M. S. Waterman",
  title     = "Identification of Common Molecular Subsequences",
  journal   = JMB,
  year      = 1981,
  volume    = 147,
  pages     = "195--197",
}

@Article{smith05,
  author    = {S. A. Smith and P. R. Stephens and J. J. Wiens},
  title     = {Replicate patterns of species richness, historical biogeography, and phylogeny in {H}olarctic treefrogs},
  journal   = {Evolution},
  year      = 2005,
  volume    = 59,
  pages     = {2433--2450}
}

@article{smith07,
  author    = "B. J. Smith",
  title     = "boa: {A}n {R} package for {MCMC} output convergence assessment and posterior inference",
  journal   = {Journal of Statistical Software},
  year      = 2007,
  volume    = 21,
  pages     = "1--37",
}

@article{snel99,
  author    = {B. Snel and P. Bork and M. Huynen},
  title     = {Genome phylogeny based on gene content},
  journal   = {Nature Genetics},
  year      = 1999,
  volume    = 21,
  pages     = {108--110},
}

@Article{sokal58,
  author    = {R. R. Sokal and C. D. Michener},
  title     = {A statistical method for evaluating systematic relationships},
  journal   = {Univ. Kans. Sci. Bull.},
  year      = 1958,
  volume    = 28,
  pages     = {1409--1438}
}

@Book{sokal69,
  author    = {R. R. Sokal and F. J. Rohlf},
  title     = {Biometry},
  publisher = {W. H. Freeman and Company},
  year      = 1969,
  address   = {New York}
}

@article{sparks04,
  author    = "J. S. Sparks and W. L. Smith",
  title     = "Phylogeny and Biogeography of Cichlid Fishes (Teleostei: Perciformes: Cichlidae)",
  journal   = {Cladistics},
  year      = 2004,
  volume    = 20,
  pages     = "501--517",
}

@Article{stadler11,
  author    = {T. Stadler},
  title     = {Simulating trees on a fixed number of extant species},
  journal   = {Systematic Biology},
  year      = 2011,
  volume    = 60,
  pages     = {?--?}
}

@Book{stanton86,
  author    = {D. Stanton and D. White},
  title     = {Constructive {C}ombinatorics},
  publisher = {Springer-Verlag},
  year      = 1986,
  address   = {New York}
}

@Article{stamatakis05,
  author    = {A. Stamatakis and T. Ludwig and H. Meier},
  title     = {{RAxML-III}: {A} fast program for maximum likelihood based inference of large phylogenetic tress},
  journal   = {Bioinformatics},
  year      = 2005,
  volume    = 21,
  pages     = {456--463}
}

@Article{steel88,
  author    = {M. A. Steel},
  title     = {Loss of information from genetic distances},
  journal   = {Nature},
  year      = 1988,
  volume    = 336,
  pages     = {118}
}

@Article{steel93,
  author    = {M. A. Steel and D. Penny},
  title     = {Distributions of tree comparison metrics --- some new results},
  journal   = {Systematic Biology},
  year      = 1993,
  volume    = 42,
  pages     = {126--141}
}

@Article{steel93a,
  author    = {M. A. Steel and D. Penny},
  title     = {Parsimony, likelihood, and the role of models in molecular phylogenetics},
  journal   = {Molecular Biology and Evolution},
  year      = 2000,
  volume    = 17,
  pages     = {839--850}
}

@Article{steel93b,
  author    = {M. A. Steel and D. Penny},
  title     = {Distributions of tree comparison metrics---some new results},
  journal   = {Systematic Biology},
  year      = 1993,
  volume    = 42,
  pages     = {126--141}
}

@Article{steel04,
  author    = {M. A. Steel and D. Penny},
  title     = {Two further links between {MP} ad {ML} under the {P}oisson model},
  journal   = {Applied Mathematics Letters},
  year      = 2004,
  volume    = 17,
  pages     = {785--790}
}

@Article{stephens00,
  author    = {M. Stephens},
  title     = {Dealing with label-switching in mixture models},
  journal   = {Journal of the Royal Statistics Society, Series B },
  year      = 2000,
  volume    = 62,
  pages     = {795--809}
}

@InProceedings{stephens03,
  author    = {M. Stephens},
  editor    = {D. J. Balding and M. Bishop and C. Cannings},
  title     = {Inference under the coalescent},
  booktitle = {Handbook of {S}tatistical {G}enetics, 2nd {E}dition},
  publisher = {John Wiley \& Sons},
  year      = 2003,
  pages     = {636--661}
}

@InProceedings{stewart99,
  author    = {W. J. Stewart},
  editor    = {W. Grassmann},
  title     = {Numerical methods for computing stationary distributions of finite irreducible {M}arkov chains},
  booktitle = {Advances in Computational Probability},
  publisher = {Kluwer Academic Publishers},
  year      = 1999
}

@Article{stoye98,
  author    = {J. Stoye},
  title     = {Multiple sequence alignment with the divide-and-conquer method},
  journal   = {Gene},
  year      = 1998,
  volume    = 211,
  pages     = {GC45--GC56}
}

@Article{strimmer96,
  author    = {K. Strimmer and A. von Haeseler},
  title     = {Quartet puzzling: {A} quartet maximum likelihood method for reconstructing tree topologies},
  journal   = {Molecular Biology and Evolution},
  year      = 1996,
  volume    = 13,
  pages     = {964--969}
}

@Article{suchard01,
  author    = {M. A. Suchard and R. E. Weiss and J. S. Sinsheimer},
  title     = {Bayesian selection of continuous-time {M}arkov chain evolutionary models},
  journal   = {Molecular Biology and Evolution},
  year      = 2001,
  volume    = 18,
  pages     = {1001--1013}
}

@Article{suchard02,
  author    = {M. A. Suchard and R. E. Weiss and K. S. Dorman and J. S. Sinsheimer},
  title     = {Oh brother, where art thou? {A} {B}ayes factor test for recombination with uncertain heritage},
  journal   = {Systematic Biology},
  year      = 2002,
  volume    = 51,
  pages     = {715--728}
}

@Article{suchard03a,
  author    = {M. A. Suchard and R. E. Weiss and K. S. Dorman and J. S. Sinsheimer},
  title     = {Inferring spatial phylogenetic variation along nucleotide sequences: {A} multiple changepoint model},
  journal   = {Journal of the American Statistics Association},
  year      = 2003,
  volume    = 98,
  pages     = {427--437}
}

@Article{suchard03b,
  author    = {M. A. Suchard and C. M. R. Kitchen and J. S. Sinsheimer and R. E. Weiss},
  title     = {Hierarchical phylogenetic models for analyzing multipartite sequence data},
  journal   = {Systematic Biology},
  year      = 2003,
  volume    = 52,
  pages     = {649--664}
}

@Article{suchard05,
  author    = {M. A. Suchard},
  title     = {Stochastic models for horizontal gene transfer: taking a random walk through tree space},
  journal   = {Genetics},
  year      = 2005,
  volume    = 170,
  pages     = {419--431}
}

@Article{suchard06,
  author    = {M. A. Suchard and B. D. Redelings},
  title     = {{Bali-Phy}: simultaneous {B}ayesian estimation of alignment and phylogeny},
  journal   = {Bioinformatics},
  year      = 2006,
  volume    = 22,
  pages     = {2047--2048}
}

@Article{sullivan05,
  author    = {J. Sullivan and P. Joyce},
  title     = {Model selection in phylogenetics},
  journal   = {Annual Review of Ecology, Evolution, and Systematics},
  year      = 2005,
  volume    = 36,
  pages     = {445--466}
}

@Book{swofford98,
  author    = {D. L. Swofford},
  title     = {{PAUP*}: {P}hylogenetic {A}nalysis {U}sing {P}arsimony and {O}ther {M}ethods},
  publisher = {Sinauer Associates, Inc.},
  year      = 1998,
  address   = {Sunderland, Massachusetts}
}

@InProceedings{swofford92,
  author    = {D. L. Swofford and W. P. Maddison},
  editor    = {R. L. Mayden},
  title     = {Parsimony, character-state reconstructions, and evolutionary inferences},
  booktitle = {Systematics, historical ecology, and North American freshwater fishes},
  publisher = {Stanford University Press},
  year      = 1992,
  pages     = {186--223}
}

@InProceedings{swofford96,
  author    = {D. L. Swofford and G. Olsen and P. Waddell and D. M. Hillis},
  editor    = {D. M. Hillis and C. Moritz and B. Mable},
  title     = {Phylogenetic inference},
  booktitle = {Molecular Systematics, 2nd edition},
  publisher = {Sinauer Associates, Inc.},
  year      = 1996,
  pages     = {407--511}
}

@Article{swofford01,
  author    = {D. L. Swofford and P. J. Waddell and J. P. Huelsenbeck and P. G. Foster and P. O. Lewis and J. S. Rogers},
  title     = {Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods},
  journal   = {Systematic Biology},
  year      = 2001,
  volume    = 50,
  pages     = {525--539}
}

@Misc{simon01,
  author       = {D. Simon and B. Larget},
  title        = {Bayesian Analysis in Molecular Biology and Evolution {(BAMBE)}},
  howpublished = {http://www.mathcs.duq.edu/larget/bambe.html},
  year         = 2001
}

@Book{sokal63,
  author    = {R. R. Sokal and P. H. A. Sneath},
  title     = {Principles of {N}umerical {T}axonomy},
  publisher = {W. H. Freeman},
  year      = 1963,
  address   = {San Francisco}
}

@Article{syvanen94,
  author    = {M. Syvanen},
  title     = {Horizontal gene transfer: evidence and possible consequences},
  journal   = {Annual Review of Genetics},
  year      = 1994,
  volume    = 28,
  pages     = {237--261}
}

%*********************************************************************************
% T
%*********************************************************************************

@Article{tamura93,
  author    = {K. Tamura and M. Nei},
  title     = {Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees},
  journal   = {Molecular Biology and Evolution},
  year      = 1993,
  volume    = 10,
  pages     = {512--526}
}

@Article{tarnas98,
   Author   = {C. Tarnas and R. Hughey},
   Title    = {{R}educed space hidden {M}arkov model training},
   Journal  = {Bioinformatics},
   Year     = {1998},
   Volume   = {14},
   Number   = {5},
   Pages    = {401--406},
   Month    = {Jun}
}

@Article{tateno82,
  author    = {Y. Tateno and M. Nei and F. Tajima},
  title     = {Accuracy of estimated phylogenetic trees from molecular data. {I}. {D}istantly related species},
  journal   = {Journal of Molecular Evolution},
  year      = 1982,
  volume    = 18,
  pages     = {387--404}
}

@Article{tavare86,
  author    = {S. Tavar{\'e}},
  title     = {Some probabilistic and statistical problems on the analysis of {DNA} sequences},
  journal   = {Lectures in Mathematics in the Life Sciences},
  year      = 1986,
  volume    = 17,
  pages     = {57--86}
}

@Article{teh06,
  author    = {Y. W. Teh and M. I. Jordan and M. J. Beal and D. M. Blei},
  title     = {Hierarchical {D}irichlet processes},
  journal   = {Journal of the American Statistical Association},
  year      = 2006,
  volume    = 101,
  pages     = {1566--1581}
}

@Article{thomas00,
  author    = {A. Thomas and N. Best and D. Spiegelhalter},
  title     = {Win{BUGS} --- A {B}ayesian modelling framework: {C}oncepts, structure, and extensibility},
  journal   = {Statistics and Computing},
  year      = 2000,
  volume    = 10,
  pages     = {325--337}
}

@Book{thompson75,
  author    = {E. A. Thompson},
  title     = {Human {E}volutionary {T}rees},
  publisher = {Cambridge University Press},
  year      = 1975,
  address   = {Cambridge, England}
}

@Article{thompson94,
  author    = {J. D. Thompson and D. G. Higgins and T. J. Gibson},
  title     = {Clustal-{W}---improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice},
  journal   = {Nucleic Acids Research},
  year      = 1994,
  volume    = 22,
  pages     = {4673--4680}
}

@article{thorne91,
  author    = {J. L. Thorne and H. Kishino and J. Felsenstein},
  title     = {An Evolutionary Model for Maximum Likelihood Alignment of {DNA} Sequences},
  journal   = JME,
  year      = 1991,
  volume    = 33,
  pages     = {114--124}
}

@article{thorne92,
  author    = {J. L. Thorne and H. Kishino and J. Felsenstein},
  title     = {Inching Toward Reality: an Improved Likelihood Model of Sequence Evolution},
  journal   = JME,
  year      = 1992,
  volume    = 34,
  pages     = {3--16}
}

@Article{thorne98,
  author    = {J. Thorne and H. Kishino and I. S. Painter},
  title     = {Estimating the rate of evolution of the rate of molecular evolution},
  journal   = {Molecular Biology and Evolution},
  year      = 1998,
  volume    = 15,
  pages     = {1647--1657}
}

@Article{thorne02,
  author    = {J. Thorne and H. Kishino},
  title     = {Divergence time and evolutionary rate estimation with multilocus data},
  journal   = {Systematic Biology},
  year      = 2002,
  volume    = 51,
  pages     = {689--702}
}

@InProceedings{tierney96,
  author    = {L. Tierney},
  editor    = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  title     = {Introduction to general state-space {M}arkov chain theory},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  publisher = {Chapman and Hall},
  year      = 1996,
  pages     = {59--74}
}

@Article{tuffley97,
  author    = {C. Tuffley and M. Steel},
  title     = {Links between maximum likelihood and maximum parsimony under a simple model of site substitution},
  journal   = {Bulletin of Mathematical Biology},
  year      = 1997,
  volume    = 59,
  pages     = {581--607}
}

@Article{tuffley98,
  author    = {C. Tuffley and M. Steel},
  title     = {Modeling the covarion hypothesis of nucleotide substitution},
  journal   = {Mathematical Biosciences},
  year      = 1998,
  volume    = 147,
  pages     = {63--91}
}

@Article{tierney94,
  author    = {L. Tierney},
  title     = {{Markov} chains for exploring posterior distributions (with discussion)}},
  journal   = {Annals of Statistics},
  year      = 1994,
  volume    = 22,
  pages     = {1701--1762}
}

@InProceedings{thorne04,
  author    = {J. Thorne},
  editor    = {R. Nielsen},
  booktitle = {Statistical Methods in Molecular Evolution},
  title     = {{B}ayesian calibration of the molecular clock},
  publisher = {Springer-Verlag},
  year      = 2004
}

%*********************************************************************************
% U
%*********************************************************************************

@Article{underhill00,
  author    = {P. A. Underhill and P. Shen and A. A. Lin and L. Jin and G. Passarino and W. H. Yang and E. Kauffman and B. Bonn\'e-Tamir and J. Bertranpetit and P. Francalacci and M. Ibrahim and T. Jenkins and J. R. Kidd and S. Q. Mehdi and M. T. Seielstad and R. S. Wells and A. Piazza and R. W. Davis and M. W. Feldman and L. L. Cavalli-Sforza and P. J. Oefner},
  title     = {Y chromosome sequence variation and the history of human populations},
  journal   = {Nature Genetics},
  year      = 2000,
  volume    = 26,
  pages     = {358--361}
}

@Article{uzzell71,
  author    = {T. Uzzell and K. W. Corbin},
  title     = {Fitting discrete probability distributions to evolutionary events},
  journal   = {Science},
  year      = 1971,
  volume    = 172,
  pages     = {1089--1096}
}

%*********************************************************************************
% V
%*********************************************************************************

@Article{vandenbussche98,
  author    = {R. A. van den Bussche and R. J. Baker and J. P. Huelsenbeck and D. M. Hillis},
  title     = {Base compositional bias and phylogenetic analyses:  {A} test of the {``Flying DNA''} hypothesis},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 1998,
  volume    = 13,
  pages     = {408--416}
}

@Article{vendetti08,
  author    = {C. Vendetti and A. Meade and M. Pagel},
  title     = {Phylogenetic mixture models can reduce node-density artifacts},
  journal   = {Systematic Biology},
  year      = 2008,
  volume    = 58,
  pages     = {286--293}
}

@Article{verdinelli95,
  author    = {I. Verdinelli and L. Wasserman},
  title     = {Computing {B}ayes factors using a generalization of the {S}avageÐ{D}ickey density ratio},
  journal   = {Journal of the American Statistical Association},
  year      = 1995,
  volume    = 90,
  pages     = {614--618}
}

@Article{vigilant91,
  author    = {L. Vigilant and M. Stoneking and H. Harpending and K. Hawkes and A. C. Wilson},
  title     = {African populations and the evolution of human mitochondrial {DNA}},
  journal   = {Science},
  year      = 1991,
  volume    = 253,
  pages     = {1503--1507}
}

@Article{vingron97,
  author    = {M. Vingron and A. von Haeseler},
  title     = {Towards integration of multiple alignment and phylogenetic tree construction},
  journal   = {Journal of Computational Biology},
  year      = 1997,
  volume    = 4,
  pages     = {23--34}
}

%*********************************************************************************
% W
%*********************************************************************************

@Article{westneat05,
  author    = {M. W. Westneat and M. E. Alfaro},
  title     = {Phylogenetic relationships and evolutionary history of the reef fish family {L}abridae},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 2005,
  volume    = 36,
  pages     = {370--390}
}

@Article{wheeler90,
  author    = {W. C. Wheeler},
  title     = {Nucleic acid sequence phylogeny and random outgroups},
  journal   = {Cladistics},
  year      = 1990,
  volume    = 6,
  pages     = {363--368}
}

@Article{whelan01,
  author    = {S. Whelan and N. Goldman},
  title     = {A general empirical model of protein evolution derived from multiple protein familes using a maximum likelihood approach},
  journal   = {Molecular Biology and Evolution},
  year      = 2001,
  volume    = 18,
  pages     = {691--699}
}

@Article{whelan03,
  author    = {S. Whelan and P. de Bakker and N. Goldman},
  title     = {Pandit: {A} database of protein and associated nucleotide domains with inferred trees},
  journal   = {Bioinformatics},
  year      = 2003,
  volume    = 19,
  pages     = {1556--1563}
}

@Article{whelan06,
  author    = {S. Whelan and P. de Bakker and E. Quevillon and N. Rodriguez and N. Goldman},
  title     = {{PANDIT}: {A}n evolution-centric database of protein and associated nucleotide domains with inferred trees},
  journal   = {Nucleic Acids Research},
  year      = 2006,
  volume    = 34,
  pages     = {D327--D331}
}

@Article{whelan07,
  author    = {S. Whelan},
  title     = {New approaches to phylogenetic tree search and their application to large numbers of protein alignments},
  journal   = {Systematic Biology},
  year      = 2007,
  volume    = 56,
  pages     = {727--740}
}

@Article{whiting94,
  author    = {M. F. Whiting and W. C. Wheeler},
  title     = {Insect homeotic transformation},
  journal   = {Nature},
  year      = 1994,
  volume    = 368,
  pages     = {696}
}

@Article{whiting97,
  author    = {M. F. Whiting and J. A. Carpenter and Q. D. Wheeler and W. C. Wheeler},
  title     = {The {S}trepsiptera problem: {P}hylogeny of the holometabolous insect orders inferred from {18S} and {28S} ribosomal {DNA} sequences and morphology},
  journal   = {Systematic Biology},
  year      = 1997,
  volume    = 46,
  pages     = {1--68}
}

@Article{wiens98,
  author    = {J. J. Wiens and M. R. Servedio},
  title     = {Phylogenetic analysis and intraspecific variation: {P}erformance of parsimony, likelihood, and distance methods},
  journal   = {Systematic Biology},
  year      = 1998,
  volume    = 47,
  pages     = {228--253}
}

@Article{wiens05,
  author    = {J. J. Wiens and J. W. Fetzner and C. L. Parinson and T. W. Reeder},
  title     = {Hylid frog phylogeny and sampling strategies for speciose clades},
  journal   = {Systematic Biology},
  year      = 2005,
  volume    = 54,
  pages     = {719--748}
}

@Article{wimmer02,
  author    = {R. Wimmer and S. Kirsch and G. A. Rappold and W. Schempp},
  title     = {Direct evidence for the {\it {H}omo-{P}an} clade},
  journal   = {Chromosome Research},
  year      = 2002,
  volume    = 10,
  pages     = {55--61}
}

@Article{wiley75,
  author    = {E. O. Wiley},
  title     = {Karl {R}. {P}opper, systematics, and classification: {A} reply to {W}alter {B}ock and other evolutionary taxonomists},
  journal   = {Systematic Biology},
  year      = 1975,
  volume    = 24,
  pages     = {233--243}
}

@Book{wiley81,
  author    = {E. O. Wiley},
  title     = {Phylogenetics: {T}he {T}heory and {P}ractice of {P}hylogenetic {S}ystematics},
  publisher = {John Wiley and Sons},
  year      = 1981,
  address   = {New York}
}

@Article{wilks38,
  author    = {S. S. Wilks},
  title     = {The large-sample distribution of the likelihood ratio for testing composite hypotheses},
  journal   = {Ann. Math. Statist.},
  year      = 1938,
  volume    = 9,
  pages     = {554--560}
}

@Article{williams71,
  author    = {W. T. Williams and H. T. Clifford},
  title     = {On the comparison of two classifications of the same set of elements},
  journal   = {Taxon},
  year      = 1971,
  volume    = 20,
  pages     = {519--522}
}

@InProceedings{woese93,
  author    = {C. R. Woese and N. R. Pace},
  editor    = {R. F. Gesteland and J. F. Atkins},
  booktitle = {The RNA World},
  title     = {Probing {RNA} structure, function, and history by comparative analysis.},
  publisher = {Cold Spring Harbor Laboratory Press},
  year      = 1993,
  pages     = {91--117}
}

@Mastersthesis{wong06,
  author    = {K. M. Wong},
  title     = {A systematic analysis of multiple alignment variability using common phylogenetic estimation parameters},
  school    = {University of California, San Diego},
  year      = 2006,
}

@Article{wong08,
  author    = {K. M. Wong and M. A. Suchard and J. P. Huelsenbeck},
  title     = {Alignment uncertainty and genomic analysis},
  journal   = {Science},
  year      = 2008,
  volume    = 319,
  pages     = {473--476}
}

@Article{wright51,
  author    = {S. Wright},
  title     = {The genetical structure of populations},
  journal   = {Ann. Eugen.},
  year      = 1951,
  volume    = 15,
  pages     = {323--354}
}

%*********************************************************************************
% X
%*********************************************************************************

@Article{xiang06,
  author    = {Q. Y. Xiang and D. T. Thomas and W. Zhang and S. R. Manchester and Z. Murrell},
  title     = {Species level phylogeny of the genus {\it {C}ornus} ({C}ornaceae) based on molecular and morphological evidence --- implications for taxonomy and {T}ertiary intercontinental migration},
  journal   = {Taxon},
  year      = 2006,
  volume    = 55,
  pages     = {9--30}
}

@Article{xiang08,
  author    = {Q. Y. Xiang and J. L. Thorne and T. K. Seo and W. H. Zhang and D. T. Thomas and R. E. Ricklefs},
  title     = {Rates of nucleotide substitution in {C}ornaceae ({C}ornales) --- pattern of variation and underlying causal factors},
  journal   = {Molecular Phylogenetics and Evolution},
  year      = 2008,
  volume    = 49,
  pages     = {327--342}
}

@article{xie11,
author = {W Xie and P. O Lewis and Y Fan and L Kuo and M.-H Chen}, 
journal = {Syst. Biol.},
title = {Improving Marginal Likelihood Estimation for {B}ayesian Phylogenetic Model Selection},
number = {2},
pages = {150--160},
volume = {60},
year = {2011}
}

%*********************************************************************************
% Y
%*********************************************************************************

@Article{yang93,
  author    = {Z. Yang},
  title     = {Maximum likelihood estimation of phylogeny from {DNA} sequences when substitution rates differ over sites},
  journal   = {Molecular Biology and Evolution},
  year      = 1993,
  volume    = 10,
  pages     = {1396--1401}
}

@Article{yang94a,
  author    = {Z. Yang},
  title     = {Maximum likelihood phylogenetic estimation from {DNA} sequences with variable rates over sites: {A}pproximate methods},
  journal   = {Journal of Molecular Evolution},
  year      = 1994,
  volume    = 39,
  pages     = {306--314}
}

@Article{yang94b,
  author    = {Z. Yang},
  title     = {Estimating the pattern of nucleotide substitution},
  journal   = {Journal of Molecular Evolution},
  year      = 1994,
  volume    = 39,
  pages     = {105--111}
}

@Article{yang95a,
  author    = {Z. Yang},
  title     = {A space-time process model for the evolution of {DNA} sequences},
  journal   = {Genetics},
  year      = 1995,
  volume    = 139,
  pages     = {993--1005}
}

@Article{yang95b,
  author    = {Z. Yang and N. Goldman and A. E. Friday},
  title     = {Maximum likelihood trees from {DNA} sequences: {A} peculiar statistical estimation problem},
  journal   = {Systematic Biology},
  year      = 1995,
  volume    = 44,
  pages     = {384--399}
}

@Article{yang95c,
  author    = {Z. Yang and S. Kumar and M. Nei},
  title     = {A new method for inference of ancestral nucleotide and amino acid sequences},
  journal   = {Genetics},
  year      = 1995,
  volume    = 141,
  pages     = {1641--1650}
}

@Article{yang96a,
  author    = {Z. Yang},
  title     = {Maximum-likelihood models for combined analyses of multiple sequence data},
  journal   = {Journal of Molecular Evolution},
  year      = 1996,
  volume    = 42,
  pages     = {587--596}
}

@Article{yang96b,
  author    = {Z. Yang},
  title     = {Phylogenetic analysis using parsimony and likelihood methods},
  journal   = {Journal of Molecular Evolution},
  year      = 1996,
  volume    = 42,
  pages     = {294--307}
}

@Article{yang97a,
  author    = {Z. Yang},
  title     = {{PAML}: {A} program package for phylogenetic analysis by maximum likelihood},
  journal   = {Computer Applications in BioSciences},
  year      = 1997,
  volume    = 13,
  pages     = {555--556}
}

@Article{yang97b,
  author    = {Z. Yang and B. Rannala},
  title     = {{Bayesian} phylogenetic inference using {DNA} sequences: a {Markov} chain {Monte Carlo} method},
  journal   = {Molecular Biology and Evolution},
  year      = 1997,
  volume    = 14,
  pages     = {717--724}
}

@Article{yang98,
  author    = {Z. Yang and R. Nielsen and M. Hasegawa},
  title     = {Models of amino acid substitution and applications to mitochondrial protein evolution},
  journal   = {Molecular Biology and Evolution},
  year      = 1998,
  volume    = 15,
  pages     = {1600--1611}
}

@Article{yang00,
  author    = {Z. Yang and R. Nielsen and N. Goldman and A. M. K. Pedersen},
  title     = {Codon-substitution models for heterogeneous selection pressure},
  journal   = {Genetics},
  year      = 2000,
  volume    = 155,
  pages     = {431--449}
}


@Article{yang02,
  author    = {Z. Yang and R. Nielsen},
  title     = {Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages},
  journal   = {Molecular Biology and Evolution},
  year      = 2002,
  volume    = 19,
  pages     = {908--917}
}

@Article{yang03,
  author    = {Z. Yang and A. D. Yoder},
  title     = {Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species},
  journal   = {Systematic Biology},
  year      = 2003,
  volume    = 52,
  pages     = {705--716}
}

@InProceedings{yang04,
  author    = {Z. Yang},
  editor    = {R. Nielsen},
  booktitle = {Statistical Methods in Molecular Evolution},
  title     = {Detecting positive selection using {PAML}},
  publisher = {Springer-Verlag},
  year      = 2004
}

@Article{yeldandi91,
  author    = {A. V. Yeldandi and V. Yeldandi and S. Kumar and C. V. Murthy and X. D. Wang and K. Alvares and M. S. Rao and J. K. Reddy},
  title     = {Molecular evolution of the urate oxidase-encoding gene in hominoid primates: nonsense mutations},
  journal   = {Gene},
  year      = 1991,
  volume    = 109,
  pages     = {281--284}
}

@Article{yoder00,
  author    = {A. D. Yoder and Z. Yang},
  title     = {Estimation of primate speciation dates using local molecular clocks},
  journal   = {Molecular Biology and Evolution},
  year      = 2000,
  volume    = 17,
  pages     = {1081--1090}
}

@Article{yu06,
  author    = {J. Yu and J. L. Thorne},
  title     = {Dependence among sites in {RNA} evolution},
  journal   = {Molecular Biology and Evolution},
  year      = 2006,
  volume    = 23,
  pages     = {1525--1537}
}

@Article{yule24,
  author    = {G. U. Yule},
  title     = {A mathematical theory of evolution, based on the conclusions of  {Dr. J. C. Wills, F. R. S.}},
  journal   = {Philosophical Transactions of the Royal Society of  London, Biology},
  year      = 1924,
  volume    = 213,
  pages     = {21--87}
}

%*********************************************************************************
% Z
%*********************************************************************************

@Article{zani00,
  author    = {P. A. Zani},
  title     = {The comparative evolution of lizard claw and toe morphology and clinging performance},
  journal   = {Journal of Evolutionary Biology},
  year      = 2000,
  volume    = 13,
  pages     = {316--325}
}

@Article{zanotto96,
  author    = {P. M. Zanotto and E. A. Gould and G. F. Gao and P. H. Harvey and E. C. Holmes},
  title     = {Population dynamics of  flaviviruses revealed by molecular phylogenies},
  journal   = {Proceedings of the National Academy of Science, U.S.A.},
  year      = 1996,
  volume    = 93,
  pages     = {548--553}
}

@Article{zhang97,
  author    = {J. Zhang and M. Nei},
  title     = {Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods},
  journal   = {Journal of Molecular Evolution},
  year      = 1997,
  volume    = 44,
  pages     = {5139--5146}
}

@Article{zhao02,
  author    = {Z. Zhao and E. Boerwinkle},
  title     = {Neighboring-nucleotide effects on single nucleotide polymorphisms: {A} study of 2.6 million polymorphisms across the human genome},
  journal   = {Genome Research},
  year      = 2002,
  volume    = 12,
  pages     = {1679--1686}
}

@InProceedings{zimmerman31,
  author    = {W. Zimmerman},
  editor    = {E. Abderhalden},
  title     = {Arbeitsweise der botanischen {P}hylogenetik und anderer {G}ruppierungswissenschaften},
  booktitle = {Handbuch der biologischen {A}rbeitsmethoden},
  publisher = {Urban and Schwarzenberg, Berlin},
  year      = 1931,
  pages     = {941--1053}
}

@InProceedings{zuckerkandl62,
  author    = {E. Zuckerkandl and L. Pauling},
  editor    = {M. Kasha and B. Pullman},
  title     = {Molecular disease, evolution, and genetic heterogeneity},
  booktitle = {Horizons in Biochemistry},
  publisher = {Academic Press, New York},
  year      = 1962,
  pages     = {189--225}
}
@Article{zuker89,
  author    = {M. Zuker},
  title     = {On Finding All Suboptimal Foldings of an {RNA} Molecule},
  journal   = {Science},
  year      = 1989,
  volume    = 244,
  pages     = {48--52}
}

@Article{zwickl04,
  author    = {D. J. Zwickl and M. T. Holder},
  title     = {Model parameterization, prior distributions, and the general time-reversible model in {B}ayesian phylogenetics},
  journal   = {Systematic Biology},
  year      = 2004,
  volume    = 53,
  pages     = {877--888}
}









