Source: http://evolution.genetics.washington.edu/phylip/software.etc1.html
Timestamp: 2019-04-25 19:50:24+00:00

Document:
The C program and MacOS 9 and MacOS X executables are available by ftp from the Indiana University Biology ftp server at ftp.bio.indiana.edu in directory molbio/evolve.
A Debian Linux executable package for fastDNAml was made available by Stephane Bortzmeyer and is maintained by Andreas Tille. It is available through its web page at http://packages.debian.org/unstable/science/fastdnaml.
Bette Korber of the Theoretical Division, Los Alamos National Laboratory , Los Alamos, New Mexico (btk (at) t10.lanl.gov) and her colleagues have released a version of fastDNAml which uses the REV (general reversible) model of DNA evolution. They used it for the results in the paper: B. Korber, M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinksy and T. Bhattacharya. 2000. Timing the ancestor of the HIV-1 pandemic strains. Science 288: 1789-1796. The program is available both in a version using the MPI Message-Passing Interface for parallel computers or a non-parallel version. It is available as C source code for Unix from the web site for the programs from that paper at http://www.santafe.edu/~btk/science-paper/bette.html.
Stamatakis, A., T. Ludwig, H. Meier, and M. J. Wolf. 2002. AxML: A fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method. pp. 21-28 in Proceedings of 1st IEEE Computer Society Bioinformatics Conference (CSB2002), Palo Alto, California, August 2002.
Stamatakis, A., T. Ludwig, and H. Meier 2003. RAxML-II: A program for sequential, parallel and distributed inference of large phylogenetic trees. Concurrency and Computation: Practice and Experience (CCPE) 16: 975-988.
Stamatakis, A., T. Ludwig, and H. Meier. 2004. RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics Advance Access published on December 17, 2004.
RAxML is available in two versions: RAxML-Light, now at verson 1.0.9, and the regular version, RAxML. RAxML-Light uses an approximate model of rate variation among sites, and can only analyze DNA sequence data, but is able to run on larger cases than the full version of RAxML. The programs are available as C source code, Windows executables, and Mac OS X executables at the Exelexis Lab software web page at http://sco.h-its.org/exelixis/software.html.
Thomas Keane (thomas.m.keane (at) nuim.ie) and Thomas Naughton (tom.naughton (at) nuim.ie), both of the Department of Computer Science of the National University of Ireland, Maynooth have released DPRML, a distributed cross-platform tree-building program that can use the idle clock cycles of machines, allowing idle time on hundreds of machines to be harnessed for tree-building. It uses the PAL Java framework. It is described in a paper: Keane, T.M., T. J. Naughton, S. A. A. Travers, J. O. McInerney, and G. P. McCormack. 2005. DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood. Bioinformatics 21: 969-974. DPRML can be downloaded from its web page at http://distributed.cs.nuim.ie/dprml.php Its authors note that it is slower than their more recent distributed phylogeny platform MULTIPHYL, and they urge use of that instead of DPRML.
T. M. Keane, T.J. Naughton, S.A.A. Travers, J.O. McInerney, and G.P. McCormack, of the Department of Computer Science at the the National University of Ireland, Maynooth, Ireland (tkeane (at) cs.nuim.ie ) have produced MultiPhyl, version 1.06, a distributed phylogeny platform enabling maximum likelihood runs across a large number of heterogeneous machines. MultiPhyl is a high-throughput implementation of a distributed phylogenetics platform that is capable of using the idle computational resources of many heteogeneous non-dedicated machines to form a phylogenetics supercomputer. It allows a user to upload hundreds or thousands of amino acid or nucleotide alignments simultaneously and perform computationally intensive tasks such as model selection, tree searching, and bootstrapping of each of the alignments. The program implements a set of 80 amino acid models and 56 nucleotide ML models and a variety of statistical methods for choosing between alternative models. It is described in the paper: Keane, T.M., T.J. Naughton, S.A.A. Travers, J.O. McInerney, and G.P. McCormack. 2005. DPRml: Distributed Phylogeny Reconstruction by Maximum Likelihood. Bioinformatics 21(7): 969-974. It is available as Java code. It can be downloaded from the downloads web site at http://distributed.cs.nuim.ie/downloads.php for the distributed Java-based platform produced by this group. The platform itself can also be downloaded from the same site. Multiphyl can also be tested by using their web server version.
Ziheng Yang of the Department of Genetics and Biometry, University College London, (z.yang (at) ucl.ac.uk) has released PAML, version 4.4, a package of programs for the maximum likelihood analysis of nucleotide or protein sequences, including codon-based methods that take into account both amino acids and nucleotides. The programs can estimate branch lengths in a phylogenetic tree and parameters in the evolutionary model such as the transition/transversion rate ratio, the gamma parameter for variable substitution rates among sites, rate parameters for different genes, and synonymous and nonsynonymous substitution rates. They can also test evolutionary models, calculate substitution rates at particular sites, reconstruct ancestral nucleotide or amino acid sequences, simulate DNA and protein sequence evolution, compute distances based on the synonymous and nonsynonymous changes, and of course do phylogenetic tree reconstruction by maximum likelihood and Bayesian Markov Chain Monte Carlo methods. The strength of the package lies in its rich implementation of evolutionary models, though Yang coments that tree-making is not a strong point of the current version. Another notable point is the availability of codon models, which Yang pioneered. The package is available as Windows executables and as C source code for Unix and MacOS X systems. An Old Versions folder in the ftp site that distributes these also contains Mac OS executables for the earlier versions 3.0a and 3.0c. See the PAML web page at http://abacus.gene.ucl.ac.uk/software/paml.html where it is available.
Gangolf Jobb (gangolf (at) treefinder.de), formerly of the Institut für Statistik of the University of München, Germany, has produced Treefinder, a maximum likelihood program for nucleotide sequence data. It makes available a variety of models of base change, including codon-position-specific models. It carries out search for best trees by its own method of tree rearrangement, and can assess statistical support for groups by either bootstrap or a local paired-sites method. All parameters of the models can be optimized by searching for the values that maximize the likelihood. The program is fast, and has both a graphical user interface and a general language in which its operation can be programmed. Trees can be interactively manipulated and constrained in various ways. Treefinder is described in a paper: Jobb, G., A. von Haeseler, and K. Strimmer. 2004. TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology 4: 18. It has been available for download from its web site at http://www.treefinder.de as executables for Windows, Mac OS X, and Linux. It requires the Java runtime environment to be present. However currently Jobb has declared himself "on strike" at this web site and asks that people first email him to discuss whether he should be compensated for his work. I do not know whether that means that the program is available for free currently, or whether he will soon start charging for it. He certainly deserves compensation for this good program.
Stéphane Guindon (currently at the University of Auckland, New Zealand, s.guindon (at) auckland.ac.nz) and Olivier Gascuel (gascuel (at) lirmm.fr) at the LIRMM, of the CNRS and the University of Montpellier II, France, have released PHYML version 3.0, a fast maximum likelihood program for nucleotide or protein sequence data. It has 6 possible DNA substition models, 5 amino acid substitution models, allowing estimation of many of the model parameters, and can allow for a gamma distribution of rates among sites and a proportion of invariable sites. It can also do bootstrapping of the trees. PHYML is described in a paper: Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704. It is available as Linux, SunOS, Windows, and Mac OS X executables from its web site in Montpellier at http://www.atgc-montpellier.fr/phyml/binaries.php, where it is also available as a web server.
Johan Nylander (Johan.Nylander (at) abc.se) has written BootPHYML version 3.4. This is a Perl script that performs bootstrapping using programs from PHYLIP , substituting PHYML for the PHYLIP program DNAML. It works with Mac OS X and Linux or Unix. It is available on a web page at Nylander's web site in Sweden.
Pierre Rioux and Tim Littlejohn, then of the Informatics Division of the Organelle Genome Megasequencing Program at the Université de Montréal (LittleJohn is currently at BioLateral Group, in Sydney, Australia, tim (at) biolateralgroup.com) made available PARBOOT (PARallel BOOTstrapping), a program that takes bootstrap sampled data sets and splits them up, submitting each to a different computer, so as to run bootstrapping quickly on networks of computers. It is intended for use with PHYLIP programs. It is available free as C source code from the Indiana University IUBIO software archive at http://microbe.bio.indiana.edu:7131/soft/iubionew/molbio/evolution/phylo/ParBoot/. It is no longer available by ftp from Montréal. It is described on a web page at the Université de Montréal at http://megasun.bch.umontreal.ca/aboutpb.html. It requires a networked system of computers with PHYLIP, a Perl interpreter, and appropriate accounts and permissions.
Friedman, N., M. Ninio, I. Pe'er, and T. Pupko. 2002. A Structural EM Algorithm for phylogenetic inference. Journal of Computational Biology 9(2): 331-353.
Ninio, M., E. Privman, T. Pupko, and N. Friedman. 2007. Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using bayesian inference of evolutionary rates. Bioinformatics 23: e136-e141.
Hudelot, C., V. Gowri-Shankar, H. Jow, M. Rattray and P. Higgs. 2003. RNA-based phylogenetic methods: Application to mammalian mitochondrial RNA sequences. Molecular Phylogenetics and Evolution 28: 241-252.
Jow, H., C. Hudelot, M. Rattray and P. Higgs. 2002. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Molecular Biology and Evolution 19: 1591-1601.
It is available as C++ source code and Linux or Windows executables from its web page at http://www.bioinf.man.ac.uk/resources/phase/.
Chen, S. C., M. Rosenberg, and B. Lindsay. 2011. MixtureTree: a program for constructing phylogeny, BMC Bioinformatics 12: 111.
David Posada (dposada (at) uvigo.es) of the Department of Biochemistry, Genetics and Immunology of the University of Vigo, Spain and Keith Crandall of the Department of Biology, Brigham Young University released Modeltest version 3.7, a program to test a hierarchy of statistical models of DNA evolution using the Likelihood Ratio Test criterion and the AIC (Akaike Information Criterion). The likelihood values are obtained by running PAUP*. MODELTEST accepts likelihood scores corresponding to 56 models of DNA substitution including whether transition and transversion rates are equal, whether rates at different sites are equal, and whether there are invariant sites. Modeltest is described in the paper: Posada, D. and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817-818. It is available as executables for Macintosh, for Windows, and source code in C for that can be compiled on many other systems. It is distributed from its web site at http://darwin.uvigo.es/software/modeltest.html. Modeltest was the basis for two further developments: the MrModeltest program which uses MrBayes and the FindModel server at Los Alamos National laboratories which is a revised version of Modeltest that uses the weighbor program to infer the trees.
Paulo Nuin (nuinp (at) mcmaster.ca) of the Department of Biology, McMaster University, Hamilton, Ontario, Canada has released MrMTgui version 1.01. This is a graphic user interface for running Modeltest and MrModeltest. It is available for Windows as executables from the MrMTgui web site at http://genedrift.org/mtgui.php. Source code of a Linux version is also available which can be compiled using the WxWindows windowing software. The Linux sources are available by accessing a svn (subversion) version-control code base, using instructions available at the above site. MrMTgui was formerly known as MTgui in the earlier version which could not access MrModeltest.
Johan Nylander (Johan.Nylander (at) abc.se) has released MrModeltest version 2.2. This is a program which is a simplified version of Modeltest 3.7. It is performs hierarchical likelihood ratio tests and calculates approximate AIC, AICc, and Akaike weights of the nucleotide substitution models currently implemented in both PAUP* and MrBayes. Version 2 has added use of four different hierarchies for the likelihood ratio tests and the selected model being printed in a MrBayes block. MrModeltest is available as an executable and source code for Windows, for Mac OS, and for Mac OS X, and as source code for Linux and Unix. It is available from Nylander's software download site at http://www.abc.se/~nylander/ in Sweden.
Johan Nylander (Johan.Nylander (at) abc.se) has written Modelfit version 1.2, and MrModelfit version 1.2. These are Perl scripts that can run (respectively) Modeltest and MrModeltest simply by typing a single command line. They are available from Nylander's software download site at http://www.abc.se/~nylander/ in Sweden.
Thomas Keane, of the Bioinformatics and Pharmacogenomics Lab of the Department of Biology, National University of Ireland, Maynooth (thomas.m.keane (at) nuim.ie) has written ModelGenerator, version 0.85. It is a Java program for model selection that selects amino acid and nucleotide substitution models using Fasta or PHYLIP alignments. It supports 56 nucleotide and 80 amino acid substitution models. It is described in the paper: Keane, T. M., C. J. Creevey, M. M. Pentony, T. J. Naughton and J. O. McInerney. 2006, Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evolutionary Biology 6: 29. It is available from its web site at http://bioinf.may.ie/modelgenerator/.
Johan Nylander (Johan.Nylander (at) abc.se) has written MrAIC verion 1.4.4. This is a Perl script that carries out AIC, AICc, BIC, and Akaike weights model comparison methods for nucleotide substitution models by invoking the PHYML program. It is distributed from Nylander's software download site at http://www.abc.se/~nylander/ in Sweden.
Sergei Kosakovsky Pond and Simon Frost of the Anitviral Research Center, University of California, San Diego and Spencer Muse of the Department of Statistics, North Carolina State University, Raleigh, North Carolina (muse (at) stat.ncsu.edu) have released HY-PHY (HYpothesis testing using PHYlogenies), version 0.99Beta. HY-PHY has general ways of enabling the user to perform a wide variety of statistical tests of different models of molecular sequence change. It is actually a higher-level programming language which enables the user to set up many different kinds of tests. The user can define their own alphabet of symbols and test any reversible subtitution model. Examples of tests that can be performed include molecular clock tests, relative rate tests, relative ratio tests, and tests of positive selection. It is described in a paper: Kosakovsky Pond, S. L., S. D. Frost, and S. V. Muse. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics 21(5): 676-679.
Although not primarily intended as a phylogeny estimation package, it also can infer trees by Neighbor-Joining and UPGMA methods, and a number of search strategies are also available for likelihood inference. HY-PHY is freely available as executables for Mac OS, for Mac OS X, for Windows, and as source code for for Unix and Linux. It is available at the HY-PHY web page at http://www.hyphy.org.
Akifumi S. Tanabe of the Division of Ecology and Evolutionary Biology, Department of Environmental Life Sciences, Graduate School of Life Sciences of Tohoku University, Japan (astanabe (at) mail.tains.tohoku.ac.jp) has released Kakusan4, a parallelized nucleotide substitution model selection script written in the Perl language for data sets with multiple partitions. Kakusan3 supports nucleotide substitution model selection on each partition and/or each codon position by AIC, AICc or BIC. Because the optimization of likelihoods is executed using BASEML, PAUP* or Treefinder and these can be run in parallel, Kakusan can take advantage of multi-core systems or multiple processor systems. The Kakusan Perl script can be run on Windows, MacOS X, Linux, FreeBSD and on other UNIX operating systems. It accepts several different input file formats. It outputs configuration files for Treefinder, MrBayes and PAUP*. It is described in the paper: Tanabe, A. S., 2007, Kakusan: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data. Molecular Ecology Notes 7: 962-964. It is available as Perl script, Windows executables and Mac OS X universal executables. It can be downloaded from its web site at http://www.fifthdimension.jp/products/kakusan/. Earlier versions, Kakusan, Kakusan2, and Kakusan3 can also be downloaded there.
Hidetoshi Shimodaira ("Shimo") of the Department of Mathematical and Computing Sciences, Tokyo Institute of Technology, Japan (shimo (at) is.titech.ac.jp) has released CONSEL version 0.1k, a package of small programs to calculate P values for tests of phylogenies. It uses output from other phylogeny programs (in particular it can use output from PAUP, PAML, PHYML, and MOLPHY) which makes available to it the sitewise log-likelihoods for some trees and the trees themselves. It uses these to carry out the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, a weighted version of the SH test, and a new "approximately unbiased" test of Shimodaira's. CONSEL is available as C source code that will compile on Linux and Unix systems that have the gcc compiler, and it is also available as a DOS executable that will run on DOS or Windows systems. It can be downloaded from its web site at http://www.ism.ac.jp/~shimo/prog/consel/index.html. It is described in a paper: Shimodaira, H. and M. Hasegawa. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 1246-1247 which cites the statistical papers describing the methods.
Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection, Systematic Biology 51 492-508.
Shimodaira, H. 2004. Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling, Annals of Statistics 32 2616-2641.
Maria Anisimova, Olivier Gascuel, and Jean-François Dufayard of the Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (LIRMM) of the Université de Montpellier II, Montpellier, France (manisimova (at) hotmail.com) have produced PHYML-aLRT (PHYML approximate Likelihood Ratio Test), version 1.1, a program to carry out likelihood ratio tests of the presence of branches in a phylogeny. PHYML-aLRT is a modification of the original PHYML program, and is designed to compute test of the reality of branches in a known phylogeny. Five branch support tests are available: (1) the bootstrap, (2) aLRT statistics, (3) aLRT parametric (Chi2-based) branch support, (4) aLRT non-parametric branch support based on a Shimodaira-Hasegawa-like procedure, and (5) a combination of these two latters supports, that is, the minimum value of both. The methods are described in the paper: Anisimova, M., and O. Gascuel. 2006. Approximate likelihood ratio test for branchs: A fast, accurate and powerful alternative. Systematic Biology 55(4): 539-552. It is available as Windows executables, Linux executables, Solaris executables, Powermac Mac OS X executables and Intel Mac OS X executables. It can be downloaded from its web site at http://atgc.lirmm.fr/phyml/alrt/ This program was of temporary usefulness; the method was made available in PHYML 3.0 and should probably be used from that program, athough these executables are still available for download.
Milne, I., F. Wright, G. Rowe, D. F. Marshal, D. Husmeier, and G. McGuire. 2004. TOPALi: Software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics 20 (11): 1806-1807.
Kim Fisker, then of the Computer Science Department at Aarhus University, Denmark released RecPars, which does a parsimony analysis of DNA sequences. It was more recently maintained by Thomas Christensen of that department. It tries to find the best phylogenies for different regions of the sequences and thereby postulating a recombination event between these segments. The method is described in a paper: Hein, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. Journal of Molecular Evolution 36: 396-406. RecPars is available as C source code for Unix. It is distributed from its web site at http://www.daimi.au.dk/~compbio/recpars/recpars.html. A web server is available there as well.
Dan Gusfield (gusfield (at) cs.ucdavis.edu) and Ren-Hua Chung (rchung (at) ucdaavis.edu), both of the Department of Computer Science at the University of California, Davis, have released PPH (Perfect Phylogeny Haplotyper). PPH takes a set of diploid genotypes for SNP (single nucleotide polymorphism) markers, and infers haplotypes for them. It does this by seeing whether it can find a set of haplotypes that resolve all diploid genotypes and that fit onto a tree without requiring any extra changes of nucleotides (in other words, they are all compatible with the same tree). The result is not only the haplotype resolution but the resulting tree, if any. The method is described in a paper: Gusfield, D., 2002 Haplotyping as perfect phylogeny: conceptual framework and efficient solutions, pp. 165-175 in Proceedings of RECOMB 2002, edited by G. Myers, S. Hannenhalli, D. Sankoff, S. Istrail, P. Pevzner et al. ACM Press, New York. The program is available as C++ and Perl source code, and as executables for Windows, for SUN SPARC Solaris, for Intel/AMD-compatible Linux, and for Mac OS X from its web site at http://wwwcsif.cs.ucdavis.edu/~gusfield/pph.html.
Minin, V. N., K. S. Dorman, and M. A. Suchard. 2005. Dual multiple change-point model leads to more accurate recombination detection, Bioinformatics 21: 3034-3042.
Suchard M. A., R. E. Weiss, K. S. Dorman. and J. S. Sinsheimer. 2003. Inferring spatial phylogenetic variation along nucleotide sequences: a multiple change-point model. Journal of the American Statistical Association 98: 427-437.
Suchard M. A., R. E. Weiss, K. S. Dorman, and J. S. Sinsheimer. 2002. Oh brother, where art thou? a Bayes factor test for recombination with uncertain heritage. Systematic Biology 51: 715-728.
Darren P. Martin and Ed Rybicki of the Microbiology Department of the University of Cape Town, Cape Town, South Africa Darrin.Martin (at) uct.ac.za) have released RDP3 (Recombination Detection Program), version 3.27, a program that applies a large number of recombination detection and analysis algorithms. This includes many of the methods used in other recombination-detection programs. In all it has about 12 different methods. The software runs under Windows and combines highly automated screening of large numbers of sequences with a highly interactive interface for examining the results of the analyses. It is described in the paper: Martin, D. P., and E. P. Rybicki. 2000. RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562-563. It is available as Windows executables. It can be downloaded from its web site at http://darwin.uvigo.es/rdp/rdp.html An older version, RDP2, is also available there, as is an "unstable" early release of RDP4.
Bette Korber of the Theoretical Division, Los Alamos National Laboratory , Los Alamos, New Mexico (btk (at) t10.lanl.gov) and her colleagues have released RevDNArates which is a version of Gary Olsen's program dnarates which uses the REV (general reversible) model of DNA evolution and calculates the maximum likelihood estimate of rate of change at each site (one parameter per site). They used it for the results in the paper: B. Korber, M. Muldoon, J. Theiler, F. Gao, R. Gupta, A. Lapedes, B. H. Hahn, S. Wolinksy and T. Bhattacharya. 2000. Timing the ancestor of the HIV-1 pandemic strains. Science 288: 1789-1796. The program is available as C source code for Unix from the web site for the programs from that paper at http://www.santafe.edu/~btk/science-paper/bette.html.
Mayrose I, D. Graur, N. Ben-Tal, and T. Pupko. 2004. Comparison of site-specific rate-inference methods for protein sequences: Bayesian methods are superior. Molecular Biology and Evolution 21: 1781-1791.
Mayrose, I., A. Mitchell, and T. Pupko. 2004. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. Journal of Molecular Evolution 60(3): 315-326.
Jianzhi George Zhang, now of the Laboratory of Genomic and Molecular Evolution in the Department of Ecology and Evolutionary Biology of the University of Michigan, Ann Arbor, Michigan (jianzhi (at) umich.edu) and Xun Gu, now at the Department of Genetics, Development, and Cell Biology at Iowa State University, Ames, Iowa (xgu (at) iastate.edu) wrote GZ-Gamma, a program for estimation of the expected number of substitutions at each amino acid or nucleotide site and the shape parameter of a Gamma distribution of rates of evolution at different sites. The program takes a phylogeny and infers the sequences at interior nodes of the tree using a Bayesian method, and then uses these to infer changes and make a histogram of changes among sites, then using that to infer the shape parameter of a Gamma distribution that fits that histogram. The method and program was described in a paper: Gu, X. and J. Zhang. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Molecular Biology and Evolution 14: 1106-1113. It is available as C source code and as MSDOS executables from the software web site of Masatoshi Nei's lab in which the work was done. A zip archive of the files can be downloaded from the link there for “Gamma”. A documentation file is also available there from the “readme” link.
Massingham, T. and N. Goldman. 2000. EDIBLE: experimental design and information calculations in phylogenetics. Bioinformatics 16: 294-295.
The program is available as C source code and as Windows and Digital Unix executables. It can be downloaded from its web site at http://www.ebi.ac.uk/goldman/info/edible.html at the EBI site.
Bret Larget, of the Departments of Statistics and Botany at the University of Wisconsin, Madison (larget (at) stat.wisc.edu) and Donald Simon of the Department of Mathematics and Computer Science, Duquesne University, Pittsburgh, Pennsylvania (simon (at) mathcs.duq.edu) have written BAMBE (Bayesian Analysis in Molecular Biology and Evolution) version 4.01a, a program for Bayesian analysis of phylogenies with DNA sequence data. It uses a prior distribution of trees and arearrangement mechanism introduced in the paper: Mau, B., M. A. Newton, and B. Larget. 1997. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Molecular Biology and Evolution 14: 717-724. The trees and parameter values are sampled by a Metropolis algorithm Markov Chain Monte Carlo sampling. The resulting posterior distribution can be used to characterize the uncertainty about not only the tree, but the parameters of the substitution model as well. The program is in C++ source code for Unix, and is distributed from his web site at http://www.stat.wisc.edu/~larget/. A Windows executable of an earlier version is also available there. The 2.03 and earlier versions are also available at a web page at Duquesne University. BAMBE is also available as a web server at the Institut Pasteur in Paris.
John Huelsenbeck (johnh (at) berkeley.edu) of the the Department of Integrative Biology of the University of California, Berkeley, and Fredrik Ronquist (Fredrik.Ronquist (at) nrm.se) of the Naturhistoriska riksmuseet, Stockholm, Sweden have written MrBayes, version 3.1.2, a program for Bayesian inference of phylogenies from nucleic acid sequences, protein sequences, and morphological characters. It assumes a prior distribution of tree topologies and uses Markov Chain Monte Carlo (MCMC) methods to search tree space and infer the posterior distribution of topologies. It reads sequence data in the NEXUS file format, and outputs posterior distribution estimates of trees and parameters. It can also use a hierarchical Bayesian framework to infer sites that are under natural selection. It allows for rate variation among sites and a variety of models of sequence evolution. MrBayes is available as a Macintosh (PowerMac) executable, a Windows executable, or as source code in C. It allows for multiple-chain Metropolis-coupled Markov Chain Monte Carlo (MC3) runs for more extensive search, and can be asked to spread jobs over a cluster of computers using the MPI message-passing interface. (Incidentally, since Bayes was Reverend Bayes, shouldn't it be named RevBayes?). MrBayes executables, source code, and documentation are available from the MrBayes web page at http://mrbayes.net.
Torsten Eriksson of the Bergius Botanical Garden, Stockholm, Sweden (torsten (at) bergianska.se) makes available MrBayes tree scanners. These are two Perl scripts that scan the output parameter files produced by MrBayes. One saves the tree corresponding to the best sample. The other saves all trees that contain a specific node (a specific grouping). They are distributed together, and available from his software distribution site at http://www.bergianska.se/index_forskning_soft.html.
Alexei Drummond, of the Department of Computer Science of the University of Auckland, New Zealand (alexei (at) cs.auckland.ac.nz) and Andrew Rambaut (a.rambaut (at) ed.ac.uk)), of the Institute of Evolutionary Biology at the University of Edinburgh, Scotland, U.K. have released Tracer, version 1.2. This is a program for analyzing the results of Bayesian sampling runs using either BEAST or MrBayes. It allows analysis of the progress of sampling the parameters. For the purposes of this listing, the relevant feature is an ability to use the trees sampled by these programs to do a Bayesian skyline plot analysis of birth and death rates of lineages. Tracer is available as a Java executable from its web site at http://tree.bio.ed.ac.uk/software/tracer/ with specific packages for Mac OS X and Windows as well.
Rabosky, D. L. 2006. Likelihood methods for inferring temporal shifts in diversification rates. Evolution 60: 1152-1164.
Rabosky, D. L., S. C. Donnellan, A. L. Talaba, and I. J. Lovette. 2007. Exceptional among-lineage variation in diversification rates during the radiation of Australia's largest vertebrate clade. Proceedings of the Royal Society of London, Series B 274: 2915-2923.
Mike Charleston (mcharles (at) it.usyd.edu.au) of the Sydney University Biological Informatics and Technology Centre, Sydney, Australia has developed Spectrum, a program for finding bipartition spectra from phylogenetic molecular and distance data, according to the method of Hendy et al. (1994) (Hadamard transforms) for moderately sized data sets (up to 18 taxa). The program also implements a branch-and-bound search for the "closest tree" - that is, the tree whose expected spectrum is closest to the spectrum derived from the observed data. Mac OS PowerMac, 68k Mac OS, and Windows executables are available from his software web site at http://www.it.usyd.edu.au/~mcharles/.
Yasuo Ina of the National Institute of Agrobiological Resources, Tsukuba, Japan developed ODEN version, a package of programs for doing distance matrix analyses on nucleotide or protein sequences. It is described in a paper: Ina, Y. 1994. ODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences. Computer Applications in the Biosciences (CABIOS) 10: 11-12. It is available free by anonymous ftp from directory pub/unix/oden on ftp.dna.affrc.go.jp as C source code for Unix systems.
Angela Lüttke and Rainer Fuchs (then of the European Molecular Biology Laboratory; Fuchs is currently at Biogen, Inc., Cambridge, Massachusetts) wrote MacT, a package of programs for Mac OS Macintoshes that compute distances and compute Neighbor-Joining phylogenies for them. The programs work on 4 through 26 sequences, and source code in Microsoft QuickBasic is provided as well as compiled executables. The package is free and is available on the molecular biology software servers. For example, it is available at the Indiana University IUBIO server at http://iubio.bio.indiana.edu/soft/molbio/mac/. It is described in a paper: Luttke, A. and R. Fuchs. 1992. MacT: Apple Macintosh programs for constructing phylogenetic trees. Computer Applications in the Biosciences 8: 591-594.
Nicholas Galtier of the University of Lyon (galtier (at) biomserv.univ-lyon1.fr) has written Phylo_win, a "graphic interface" for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and can bootstrap with any of them. Many distances can be used including Jukes and Cantor, Kimura, Tajima and Nei, Galtier and Gouy (1995), LogDet for nucleotidic sequences, Poisson correction for protein sequences, Ka and Ks for codon sequences. Species and sites to include in the analysis are selected by mouse. Reconstructed trees can be drawn, edited, printed, stored, evaluated according to numerous criteria. Taxonomic species groups and sets of conserved regions can be defined by mouse in both tools and stored into sequence files, thus avoiding multiple data files. It is entirely mouse-driven. Most usual sequence file formats are read: CLUSTAL, FASTA, PHYLIP, MASE. It runs under X windows on many Unix workstations. It is described in the paper: Galtier, N., M. Gouy, and C. Gautier. 1996. SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Computer Applications in the Biosciences 12: 543-548. Phylo_win is now considered by Galtier to have been superseded by his program SeaView. Phylo_win is distributed as C source code (to compile it one needs the NCBI Vibrant tool kit). It is also available as executables for SunOS, Solaris, SGI Unix, IBM RISC Unix, Linux, HP/UX, and DEC Alpha (Digital Unix). It can be fetched from its web page at http://pbil.univ-lyon1.fr/software/phylowin_legacy.html. It can also be obtained by anonymous ftp from biom3.univ-lyon1.fr in directory pub/mol_phylogeny. A Digital OpenVMS executable is also available as http://www.tmk.com/ftp/vms-freeware/mathog/.
Strimmer, K. and A. von Haeseler. 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 13: 964-969.
Strimmer, K., and A. von Haeseler. 1997. Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proceedings of the National Academy of Sciences (USA) 94: 6815-6819.
Schmidt, H.A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18: 502-504.
TREE-PUZZLE supports all popular models of sequence evolution of nucleotides and proteins, and can take rate heterogeneity among sites into account. It computes pairwise maximum likelihood distances for many different models of sequence evolution (TN, HKY, F84, SH, Dayhoff, JTT, mtREV24, BLOSUM62, WAG, and VT), and estimates parameters of the models. It can estimate maximum-likelihood branch-lengths for user-specified trees and perform likelihood ratio tests of clockness as well as Kishino-Hasegawa-Templeton tests. The program is written in ANSI C and is compatible with PHYLIP files. The current version also has features for parallel computation using the MPI message-passing interface, if this is available. Precompiled executables are distributed for Mac OS, Windows, and Linux. For Unix and VMS systems files for automated compilation are provided. A version capable of parallel execution is also available. TREE-PUZZLE is available from the TREE-PUZZLE web page at http://www.tree-puzzle.de. A number of places that mirrors of the distribution, or older versions, are available are listed there. Its online manual can be downloaded at http://www.tree-puzzle.de/manual.html.
Huson, D. H. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 68-73.
Huson, D. H. and Bryant, D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23(2): 254-267.
SplitsTree4, a Java version which can run under Linux, Windows, and Mac OS X.
SplitsTree 2.4, for Mac OS.
Igor Kuznetsov and Pavel Morozov, then of the Institute of Cytology and Genetics, Novosibirsk, Russia produced GEOMETRY, a package for nucleotide sequence analysis using the method of statistical geometry in sequence space. Kuznetsov (ikuznetsov (at) albany.edu) is currently at the Department of Epidemiology and Biostatistics at the State University of New York in Albany, Morozov (pm259 (at) columbia.edu) is currently at the Irving Cancer Research Center at Columbia University. The method is described in this paper: Eigen, M., R. Winkler-Oswatitsch, and A. Dress. 1988. Statistical geometry in sequence space: A method of quantitative comparative sequence analysis, Proc. Natl. Acad. Sci. USA 85: 5913-5917. The program is described in the article: Kuznetsov, I. and P. Morozov. 1996. GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space. Computer Applications in the Biosciences (CABIOS) 12: 297-301. The package uses the same data formats for sequence and tree input as the ones used in the VOSTORG package. GEOMETRY is available as a DOS executable. It is available for downloading by ftp from the EMBL file server ftp.ebi.ac.uk in directory pub/software/dos as file geom.zip.
Vincent Berry of the LIRMM, Université de Montpellier, France (vberry (at) lirmm.fr) has released PhyloQuart version 1.4, a package of programs inferring phylogenies from quartets. It is able to use either nucleotide sequences or distances. It implements the Q* method of tree reconstruction, which is inspired by the work of Bandelt and Dress, and is described in the paper: Berry, V. and O. Gascuel. 2000. Inferring evolutionary trees with strong combinatorial evidence. Theoretical Computer Science 240: 271-298. PhyloQuart is available as C source code which can be compiled on Unix systems, from its web site at http://www.lirmm.fr/~vberry/PHYLOQUART/phyloquart.html.
Vinh, L. S. and A. von Haeseler. 2004. IQPNNI: Moving fast through tree space and stopping in time. Molecular Biology and Evolution 21: 1565-1571.
Bui Quang Minh,, B. Q. L. S. Vinh, A von Haeseler and H. A. Schmidt. 2005. pIQPNNI: Parallel reconstruction of large maximum likelihood phylogenies. Bioinformatics 21(19): 3794-3796.
Minh, B. Q., L. S. Vinh, H. A. Schmidt, and A. von Haeseler. 2006. Large maximum likelihood trees. Proceedings of the NIC Symposium 2006 pp. 357-365, Forschungszentrum Jülich, Germany.
Willson, S. J. 1998. Building phylogenetic trees from quartets by using local inconsistency measures . Molecular Biology and Evolution 16: 685-693.
The programs are in C and are described as having successfully been compiled on Mac OS systems using the Codewarrior C compiler. Mac OS executables are also provided. The programs are available at Willson's software web site at http://www.public.iastate.edu/~swillson/software.html.
James Lake of the Department of Molecular, Cell and Developmental Biology of the University of California, Los Angeles (lake (at) mbi.ucla.edu) has released Gambit, which implements a method called Boostrapper's Gambit. The method involves bootstrap sampling sequences, computing trees for quartets of species, and assembling larger trees out of quartets that have significant boostrap support. One of the methods available to estimate trees from the quartets is paralinear (LogDet) distances. Other distance methods and parsimony are also available. The Bootstrapper's Gambit method is described in a paper: Lake, J. A. 1995. Calculating the probability of multitaxation evolutionary trees: Bootstrappers gambit. Proceedings of the National Academy of Sciences, USA 92: 9662-9666. The program is available as a DOS executable, free as a beta release to noncommercial users on a trial basis until January 1, 2003. (It is unclear from the web site whether a free version is to be available to noncommercial users after that point -- a previous deadline was extended). Commercial users are asked to pay $50 on a shareware basis. The program is available at its web site at http://genomics.ucla.edu/gambit/.
Bandelt H.-J., P. Forster, B. C. Sykes, and M. B. Richards. 1995. Mitochondrial portraits of human populations using median networks. Genetics 141: 743-53.
Bandelt, H-J., P. Forster, and A. Röhl. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48.
The program is available for free as a Windows executable from Fluxus Engineering at its web site at http://www.fluxus-engineering.com/sharenet.htm.
Mike Hendy, Katharina T. Huber, Michael Langton, Vincent Moulton, and David Penny have written Spectronet version 1.27, a program that computes a collection of weighted splits or partitions and allows the user to interactively analyze the results with a series of tools. Hendy and Penny are at Massey University, New Zealand (m.hendy (at) massey.ac.nz and d.penny (at) massey.ac.nz), Huber and Moulton are at the School of Computational Science of the University of East Anglia, U.K. (Katharina.Huber (at) cmp.uea.ac.uk and Vincent.Moulton (at) cmp.uea.ac.uk). Spectronet can read molecular sequence or discrete character data, compute splits by Hadamard conjugation or directly, compute and display compatibility matrices of characters, make reduced median networks, and plot networks by making a Lentoplot. Spectronet is described in a paper: Huber, K. T., M. Langton, D. Penny, V. Moulton and M. Hendy. 2002. Spectronet: A package for computing spectra and median networks. Applied Bioinformatics 1: 159-161. It is available as a Windows executable from its web site at http://awcmee.massey.ac.nz/spectronet/index.html.
Jin, G., L. Nakhleh, S. Snir, and T. Tuller. 2006. Maximum likelihood of phylogenetic networks. Bioinformatics 22(21): 2604-2611.
Jin, G., L. Nakhleh, S. Snir, and T. Tuller. 2007. Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23: e123-e128.
Hey J, and R. Nielsen, 2007, Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences USA 104(8): 2785-2790.
It allows Bayesian inference from a number of loci, each assumed to be without intra-locus recombination. It can use a DNA mutation model, a stepwise microsatellite mutation model, or an infinite-sites model. The program estimates the population sizes, the times of divergence, each relative to the mutation rate. It can also estimate growth rates of population sizes after speciation. IMa2 is distributed as a Windows executable with generic C source code that can easily be compiled on Unix systems including Mac OS X. It is available from its web page at the Hey lab web site, http://genfaculty.rutgers.edu/hey/software#IMa2. Earlier versions, IMa and IM, are also available there.
Liu, L. and D. K. Pearl. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56: 504-514.
Edwards, S. V., L. Liu, and D. K. Pearl. 2007. High resolution trees without concatenation. Proceedings of the National Academy of Sciences 104: 5936-5941.
Liu, L., D. K. Pearl, R. T. Brumfield, and S. V. Edwards. 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62: 2080-2091.
The two-cluster test is essentially the relative rate test for many sequences. The branch length test is the test of rate difference for each sequence under the tree root from the average rate of all sequences. The tests are described in: Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized trees. Molecular Biology and Evolution 12: 823-33. The programs are available as C source code and also as DOS executables. They are distributed (as a compressed tar archive of the source code with examples and documentation, and also as a self-extracting archive of sources and DOS executable) They are available at Naoko Takezaki's software web site at http://www.kms.ac.jp/~genomelb/takezaki.eng.html#software and also at the Nei lab software web site at http://www.bio.psu.edu/people/faculty/nei/software.htm. They are also available at by ftp from the IUBio archive at http://iubio.bio.indiana.edu/soft/molbio/evolve/lintr/.
Andrew Rambaut (a.rambaut (at) ed.ac.uk)), of the Institute for Evolutionary Biology, University of Edinburgh, Scotland, and formerly of the Department of Zoology, University of Oxford, has written TipDate version 1.2. TipDate is an application for estimating the rate molecular evolution (and hence a time-scale) for a phylogeny consisting of dated tips. These will most frequently be from viruses or other fast-evolving pathogens that have been isolated over a range of dates. The program can also return the likelihood for the simple molecular clock model (i.e., assuming that all sequences are contemporary), for a model in which rates of change at different times are drawn from a distribution, or the non-clock model. These are useful for likelihood ratio tests of the fit of the model to the data. TipDate is described in a paper: Rambaut, A. 2000. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics 16: 395-399. TipDate is available as Mac OS executables and as source code for Linux or Unix from the IUBIO software site at http://microbe.bio.indiana.edu:7131/soft/iubionew/molbio/evolution/evolve/TipDate/. It is also available in a web-based server version from the Pasteur Institute server.
Hein, J. J. 1990. A unified approach to phylogenies and alignments. Methods in Enzymology 183: 625-644.
Hein, J. J. 1994. TreeAlign. pp. 349-364 in Computer Analysis of Sequence Data. edited by A. M. Grffin and H. G. Griffin. Humana Press, Tolowa, New Jersey.
TreeAlign is available as C source code. It uses enough memory to run that it will not be practical on older desktop systems. It is available by anonymous ftp at the European Bioinformatics Institute molecular biology software distribution site ftp.ebi.ac.uk in directories pub/software/unix and pub/software/vms.
ClustalW which has a character-mode interface, in which the user types responses to choose options from a menu.
ClustalX which has a graphical user interface.
Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
Jeanmougin, F., J. D. Thompson, T. J. Gibson, M. Gouy, and D. G. Higgins. 1998. Multiple sequence alignment with Clustal X. Trends in Biochememical Sciences 23: 403-405.
Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24: 4876-4882.
Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using CLUSTAL for multiple sequence alignments. Methods in Enzymology 266: 383-402.
Thompson, J.D., D. G. Higgins and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
ClustalW is available from its main distribution page at http://www.clustal.org. The downloads of the current version there are also available by ftp from the European Bioinformatics Institute ftp server.
For the older ClustalV, there exists a Macintosh Hypercard stack, ClustToTree, that can convert its tree files to Newick Standard format (used by many other programs). ClustToTree is made available by Kai-Uwe Fröhlich at the University of Graz, Austria at http://aaa-proteins.uni-graz.at/Archiv/ClustToTreecomp.html.
ClustalW is made available on web servers by the Genebee web server at the Belozersky Institute in Moscow, and at the European Bioinformatics Institute.
Ward Wheeler of the Division of Invertebrate Zoology, American Museum of Natural History, New York (wheeler (at) amnh.org) and David Gladstein (gladstein (at) gladstein.org) have written MALIGN, version 2.7, a parsimony-based alignment program for molecular sequences. It implements the original suggestion by Sankoff, Morel, and Cedergren (1973) that alignment and phylogenies could be done at the same time by finding that tree that minizes the total alignment score along the tree. Jotun Hein's program TreeAlign (mentioned above) is another, more approximate but possibly faster, attempt to implement the Sankoff-Morel-Cedergren suggestion. MALIGN is one of the only programs to calculate this optimality criterion exactly (Wheeler and Gladstein's other program POY is the other). MALIGN is described in a paper: Wheeler, W. C. and D. S. Gladstein. 1994. MALIGN - A multiple sequence alignment program. Journal of Heredity 85: 417-418. MALIGN is available from its download web site at the Program in Scientific Computation of the American Museum of Natural History at http://research.amnh.org/scicomp/projects/malign.php. It is available as C source code and as binaries for Linux, Windows, Sun Solaris, SGI, and HPUX. The C source code is distributed in two forms, the ordinary one and a special version for parallel computation.
MiraiBio, a Hitachi Software company DNASIS, a general-purpose DNA and protein sequence analysis system, produced by Molecular Biology Insights, Inc. of Cascade, Colorado (but sold through Hitachi). It has many functions including primer design, plasmid maps, contig assembly, alignment, database searching, and many kinds of protein plots. For our purposes what is relevant is the ability to do multiple sequence alignment by the Higgins-Sharp method of progressive sequence alignment (the one used in ClustalV), with one of the results being a UPGMA tree based on pairwise sequence alignment scores. DNASIS is available from MiraiBio as version 3.0 (called DNASIS MAX) Windows executables, including a demo version at its web site at http://www.miraibio.com/dnasis-max/dnasis-max-overview.html. Prices are not stated there -- there is Order form that can be sent to them by email. It was formerly also available from MBI, and at that time a Windows version cost $1,895 and a Mac OS X version cost $2,995 for a 1-10 user network license.
Karl Nicholas (karlnicholas (at) hotmail.com) with help from Hugh Nicholas (nicholas (at) psc.edu) of the National Resource for Biomedical Supercomputing (NRBSC; www.nrbsc.org) at the Pittsburgh Supercomputing Center has produced GeneDoc, version 2.6.0.2, a program for the shading and editing of multiple sequence alignments. Its reads .MSF files and Fasta Files. The alignment can be edited by changing the position of residues in the sequences. GeneDoc includes scoring functions to assist in determining whether your aligment changes are improving the score. Support for obtaining a score via sum-of-pairs or by a phylogenetic tree is included. Phylogenetic trees can be built with either the GUI interface or imported NEXUS or PHYLIP format tree descriptions. The program runs on Windows and both 16-bit and 32-bit executables are distributed. The source code is also available there. It can be downloaded from its Web site at http://www.nrbsc.org/gfx/genedoc/gddl.htm A Windows NT version for Digital Alpha processors was formerly available from Russell Malmberg at the Botany Department of the University of Georgia but is not currently in distribution.
Varón, A., L. S. Vinh, and W. C. Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics 26: 72-85.
Wheeler, W. C. 1999. Fixed character States and the optimization of molecular sequence data. Cladistics 15: 379-385.
Wheeler, W. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics 12:1-9.
POY is available in C source or in executables for Linux, Mac OS X, and Windows. It is distributed from its download web site at the Program in Scientific Computation of the American Museum of Natural History at http://research.amnh.org/scicomp/projects/poy.php.
Russell Doolittle (rdoolittle (at) ucsd.edu) and Dafei Feng, of the Section of Molecular Biology of the Division of Biological Sciences of the University of California at San Diego, released ALIGN in 1990. A version for Macintoshes was coded by Peter Markeiwicz. ALIGN implements the "progressive alignment" strategy described in their paper: Feng, D.-F. and R. F. Doolittle. 1987. Progressive sequence aligment as a prerequisite to correct phylogenetic trees. Journal of Molecular Evolution 25: 351-360. This is also the basis for the Clustal family of programs as well as the (formerly distributed) Pileup program in the GCG package. The ALIGN program can align as well as print out a tree (which does not have branch lengths). It uses Doolittle's own formats, and so three other programs are included with ALIGN to convert formats. The programs are distributed by ftp from the EBI ftp software server at ftp.ebi.ac.uk in directory pub/software/mac as file align.hqx. A set of C source programs presumably equivalent to these is also made available by Milton Saier at UCSD on a web page at http://www-biology.ucsd.edu/~msaier/transport/software.html.
Redelings B. D, and M. A. Suchard 2005. Joint Bayesian estimation of alignment and phylogeny, Systematic Biology 54(3): 401-418.
Suchard, M. A. and B. D. Redelings. 2006. BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22: 2047-2048.
Katoh, K. and H. Toh. 2007. PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences. Bioinformatics 23: 372-374.
Katoh, K., K. Kuma, H. Toh and T. Miyata, 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511-518.
It is available as C++ source code, Windows executables, Linux executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://align.bmr.kyushu-u.ac.jp/mafft/software/ A web server is also available there.
Edgar, R. C. and K. Sjolander. 2003. SATCHMO: Sequence alignment and tree construction using hidden Markov models, Bioinformatics 19(11): 1404-1411.
It is available as C++ source code, Windows executables and Linux executables. It can be downloaded from the LOBSTER web site at http://www.drive5.com/lobster/ There is also a web server available to run the program.
Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5): 1792-1797.
Edgar, R. C. 2004. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5 113.
There is also web server of MUSCLE available at Kimmen Sjölander's group, but it does not return the trees inferred.
Pietro Liò, of the Computer Laboratory at the University of Cambridge (Pietro.Lio (at) cl.cam.ac.uk), has written PASSML and PASSML_TM, which use likelihood methods with Hidden Markov models to infer phylogeny and also secondary structure from protein data. PASSML is for general proteins and PASSML_TM is for membrane proteins. The methods used are described in the papers: Goldman, N., J. L. Thorne, and D. T. Jones. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149: 445-458, PASSML is described in the paper: Liò, P., N. Goldman, J. L. Thorne and D. T. Jones. 1998. PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics 14: 726-733, and PASSML_TM is described in the paper: Liò, P. and N. Goldman. 1999 Using protein structural information in evolutionary inference: transmembrane proteins. Molecular Biology and Evolution 16: 1696-1710. The programs are available as ANSI C source code. The source code is available via its web page at http://www.ebi.ac.uk/goldman/hmm/passml.html.
Rod Page (r.page (at) bio.gla.ac.uk), of the Division of Environmental and Evolutionary Biology of the University of Glasgow has written COMPONENT version 2.0, a program for Windows systems for comparing cladograms for use in phylogeny and biogeography studies. It has many tree comparison and consensus methods, and far more features for biogeographic studies (such as comparing species and area cladograms) than any other package. It also can generate random trees. It runs under Windows 3.0 or higher. There is a review of the program in: Slowinksi, J. 1993. Review of Component, Version 2.0, by Roderick D. M. Page. Cladistics 9: 351-353. COMPONENT is available free from its web site at http://taxonomy.zoology.gla.ac.uk/rod/cpw.html. Source code in Pascal and documentation (as PDFs) are also available there. A very early development Macintosh version ("COMPONENT Lite") is available from the COMPONENT Lite web site at http://taxonomy.zoology.gla.ac.uk/rod/cplite/guide.html.
Rod Page(r.page (at) bio.gla.ac.uk), of the Division of Environmental and Evolutionary Biology of the University of Glasgow and Michael Charleston (mcharles (at) it.usyd.edu.au) of the Biological Informatics and Technology Centre of the School of Information Technologies of the University of Sydney, Sydney, Australia have written TREEMAP, version 3, a free program for comparing host and parasite phylogenies. It allows you to interactively compare host and parasite trees, construct reconstructions of the history of the association, and perform some simple randomisation tests of hypotheses of cospeciation. It also can use Charleston's "Jungles" method to fit parasite trees to host trees by parsimony. That method is described in his paper: Charleston, M. A. 1998 Jungles: A new solution to the host/parasite phylogeny reconciliation problem. Mathematical Biosciences 149: 191-223. For a description of the method used by TreeMap, see Page, R.D.M. 1994. Parallel phylogenies: Reconstructing the history of host-parasite assemblages. Cladistics 10: 155-173. It can also estimate the number of randomized parasite trees that map as well to the host tree as does the original parasite tree. The program is available as a Java executable, which can be downloaded from its web site at http://www.it.usyd.edu.au/~mcharles/software/treemap/treemap3.html. A beta release executable for Mac OS of version 2.0, called version 2.0β, is available at the Treemap 2.0β web site at http://www.it.usyd.edu.au/~mcharles/software/treemap/treemap.html. An earlier version, 1.0, is available as an executable for Mac OS or as an executable for Windows PCs. They can be downloaded from its WWW site: http://taxonomy.zoology.gla.ac.uk/rod/treemap.html.
Fredrik Ronquist (Fredrik.Ronquist (at) nrm.se) of the Naturhistoriska riksmuseet, Stockholm, Sweden has released DIVA version 1.2, a program for DIspersal Vicariance Analysis. It is for analyses in historical biogeography, where one is reconstructing the distribution history of a group of organisms from the distribution areas of extant species and their phylogeny. It is a parsimony-style analysis based on optimization of the numbers of dispersal and extinction events, where one assumes that speciations divide species ranges allopatrically. It does not make any assumption about the hierarchical nature of vicariance events. It was formerly available as either a Windows executable or a Mac OS executable from its web page at http://www.ebc.uu.se/systzoo/research/diva/diva.html. Currently there is some download, not well described, including perhaps source code, available from the Sourceforge site at http://diva.sourceforge.net/.
Fredrik Ronquist (Fredrik.Ronquist (at) nrm.se) of the Naturhistoriska riksmuseet, Stockholm, Sweden has written TreeFitter version 1.0. It fits parasite trees to a host tree, and can also use them to infer the best host tree. The program, which has many options, uses an event-based parsimony method, which penalizes events using penalties chosen to reflect their improbability. The NEXUS file format is used for the tree files. It is available from its web site at http://www.ebc.uu.se/systzoo/research/treefitter/treefitter.html as either a Windows executable or a Mac OS executable. An on-line manual is available at the web site.
Athanasia C. Tzika, Raphaël Helaers, and Michel Milinkovitch of the Laboratory of Artificial and Natural Evolution (LANE) of the Department of Zoology and Animal Biology at the University of Geneva, Switzerland, and Yves Van de Peer, of the Department of Plant Systems Biology of the University of Gent, Belgium (info (at) mantisdb.org) or (Michel.Milinkovitch (at) unige.ch) have produced MANTiS version 1.1, a program using molecular databases to reconstruct gene duplications and losses . MANTiS builds a relational database integrating, in a phylogenetic framework, all Ensembl genes, corresponding PANTHER molecular functions and biological processes, as well as GNF, e-genetics, and HMDEG expression data. It makes use of the Ensembl ortholog/paralog prediction pipeline to reconstruct gene duplication events, and implements a dynamical programming approach for the mapping of gene gains, duplications, and losses on the phylogenetic tree.
Nielsen, R. 2002. Mapping mutations on phylogenies. Systematic Biology 51: 729-739.
Huelsenbeck, J. P., R. Nielsen, and J. P. Bollback. 2003. Stochastic mapping of morphological characters. Systematic Biology 52: 131-158.
Bollback, J. P. 2006. SIMMAP: Stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7:88.
SIMMAP is a Mac OS X executable, available from its web page at http://www.simmap.com at the University of Copenhagen.
Xun Gu, of the Department of Genetics, Development and Cell Biology and the Center for Bioinformatics and Biological Statistics at Iowa State University, Ames, Iowa (xgu (at) iastate.edu) has release Mgenome version 1.0. It finds trees for multiple genome rearrangement by signed reversals. For a collection of genomes represented by signed permutations of genes, it finds a tree that connects all given genomes by reversal paths such that the number of all signed reversals is as small as possible. The methods seem to be described in a paper: Wu, S., and X. Gu. 2003. Algorithms for multiple genome rearrangement by signed reversals. Pacfic Symposium on Biocomputing 8: 363-74, although the paper does not refer to the program. The paper is available as a PDF at the Gu lab web site. The program is available as a Windows executable at the Gu lab software web site at http://xungulab.com/software.html.

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