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Old Phylogeny Programs
(ones no longer distributed)

The programs described in this web page were formerly listed in the Phylogeny Programs web pages but are ones which are no longer distributed. The entries describing them have been moved here. The web links and ftp addresses in these listings typically do not work any longer. It may be possible to track down the authors of these packages and get information directly from them. I have added comments at the top of some entries as to what I know about its status.

(This program is one that is still in distribution. It has been removed from the list, not because there is anything wrong with it, but because I have reconsidered where the boundary of this listing is. As a data-conversion utility it lies outside it.)

[Tonex icon] Mauro J. Cavalcanti (maurobio  (at), o f the Departamento de Biologia Geral, Universidade Santa Ursula, Rio de Janeiro, Brazil, has written Tonex, a data set translation program for converting Hennig86 data sets into NEXUS format. It is available as MSDOS and Windows executables and as Turbo Pascal 7.0 source code at its web site at .

Not sure this one has been in distribution any time in the last 10 years.

J. S. Farris and Mary Mickevich earlier released a package of phylogeny programs, PHYSYS, which, at about $5,000, was extremely expensive (in my opinion, which is certainly a biased one). I am not sure whether, from whom, or under what conditions it is still available.

Kevin Nixon has withdrawn ClaDOS: it is replaced by his more recent program WINCLADA which incorporates the features of ClaDOS and of another program, DADA.

ClaDOS, an interactive program which allow s rearrangement of trees and their evaluation, mapping of characters into them, and more, is available for DOS systems from Kevin Nixon, L. H. Bailey Hortorium, Cornell University, 467 Mann Library, Ithaca, New York 14853. Rumor has it that the cost is in the vicinity of $55 US.

I do not know whether these programs are being distributed right now, and if so, from where. Zharkikh is now at Myriad Genetics in Salt Lake City, Utah.

Andrey Zharkikh (zharkikh  (at) ), (then) of the Genetics Centers at the University of Texas at Houston, has written a series of Unix programs to carry out various phylogeny methods. They are easily compiled on standard Unix C compilers. They include programs for

These are available by World Wide Web from or by anonymous ftp from in directory pub/zharkikh/bootstrap.

Lake is of course still at UCLA. I do not think this program is currently publicly distributed.

James Lake (lake  (at) distributes Evomony, a program for using the "evolutionary parsimony" (invariants) method for inferring phylogenies from DNA or RNA sequences. It runs on 286 or higher DOS systems with at least 500k bytes of memory. A Macintosh version was also contemplated. I do not know what the current distribution arrangements are. Lake's address is Department of Biology, University of California, Los Angeles, California 90024.

There is no sign that Fujitsu still distributes this package, which is a version of a phylogeny program called IDEN that is used at the National Institute of Genetics, Japan (but is not in general distribution).

Fujitsu Ltd. ("a $21 billion [now it's 37.7 billion] global leader in advanced computer, telecommunications, and electronic devices") sells a Fujitsu S family workstation complete with a program, SINCAIDEN, which allows "experimental researchers, even those unfamiliar with such analyses, [to] easily create phylogenetic trees in their own laboratories." The program also allows searches of the major nucleic acid sequence and protein databases (the ad I saw does not make it clear whether these databases are provided with the workstation). The methods available are UPGMA, neighbor-joining, Farris's (Distance Wagner) and the modified Farris distance matrix methods. The workstation is SPARC compatible and runs SunOS. The SINCAIDEN program was developed by the group at the National Institute of Genetics, Japan under Dr. Takashi Gojobori. Fujitsu Ltd. may be contacted at 21-8, Nishi-Shinbashi 3- chome, Minato-ku, Tokyo 105, Japan (phone 81-3-3437-5111 ext. 2831, fax 81-3- 5472-4354), or in the U.S. at Fujitsu America Inc., 3055 Orchard Drive, San Jose, California 95134-2017 (phone 1-408-432-1300 ext. 5168, fax 1-408-434- 1045). There is a web page in Japanese at Several years ago the price of SINCAIDEN (with workstation) was $28,000.

This teaching program seems no longer to be in distribution (it is not clear that its author decided this).

[Systack icon here] Arnold G. Kluge (akluge  (at), of the Department of Biology of the University of Michigan, has written Systack, a teaching program designed to teach the principles of synapomorphy/homology analysis in the context of chordate phylogeny. It implements a hierarchical filing system in the form of a phylogeny, with character information available on chordates and with users able to add new characters. It is a Hypercard stack for Macintosh computers, and is available free for noncommercial use. A Web site is available at to download it.

This program has been withdrawn because it is now contained within their later system vCEBL.

Allen Rodrigo of the Computational and Evolutionary Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand (a.rodrigo  (at) distributes sUPGMA (Serial sample UPGMA). It reconstructs evolutionary histories/genealogies under the assumption of a molecular clock when sequences are obtained serially in time. Input is a distance matrix. sUPGMA can also carry out the ordinary UPGMA, WGPMA and Neighbor-Joining methods. sUPGMA is a Java applet. It is available for downloading from its web site at"> or for use as a server. sUPGMA runs under Netscape Communicator 4.7 or Microsoft Internet Explorer 5 on PCs running Windows 95/98, and Microsoft Internet Explorer 4.5 on Macintoshes. It can also be run in standalone mode if you have a Java runtime engine.

Andrew Rambaut has retired SPOT as he considers it obsolete in view of the features of PAUP*.

[SPOT icon here] Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) and Nick Grassly, currently of the Zoologisches Institut, Universität München (grassly  (at), have written SPOT (Sequence Parameters Of Trees). SPOT is a program that will calculate the likelihood of a given tree topology for a set of aligned nucleotide sequences. For each topology, SPOT will estimate the maximum likelihood values of branch lengths and other parameters of the model of nucleotide evolution that has been chosen. Such parameters include the ratio of transitions to transversions (TS/TV ratio) and relative rates of substitution at different codon positions. Branch lengths can also be constrained to assume a molecular clock hypothesis. Multiple datasets and multiple trees can be analysed which is useful for performing Monte Carlo simulations of hypothesis (parametric bootstraps). Although SPOT does not estimate tree topology, an accompanying program, SPOTSHELL, will iterate between fastDNAml and SPOT until the maximum likelihood parameters and topology has been found (or at least something close to it). SPOT is available as C source code for Unix workstations, or as Macintosh sources and executables. It can be obtained from the SPOT Web page at

Lyons-Weiler has moved to the University of Pittsburgh. I suspect that RASA will be made available there in the near future.

[RASA icon here] James Lyons-Weiler of the Biological Sciences Department of the University of Massachusetts, Lowell (James_LyonsWeiler  (at) UML.EDU) has written RASA, version 2.5, software for Macintoshes that will perform "Relative Apparent Synapomorphy Analysis", a test for the presence of phylogenetic signal in any type of discrete character data matrix (morphological or molecular). The RASA program carries out the test and plots the results. RASA is menu-driven. The test compares the observed and null rates of increase in cladistic similarity among pairs of taxa predicted by an increase in the phenetic similarity among taxon pairs. The test is described in a paper: Lyons-Weiler, J., G.A. Hoelzer, and R.J. Tausch. 1996. Relative Apparent Synapomorphy Analysis (RASA) I: the statistical measurement of phylogenetic signal. Molecular Biology and Evolution 13: 749-757, the taxon variance plot tool in RASA was described in the paper: Lyons-Weiler, J., and G.A. Hoelzer. 1997. Escaping from the Felsenstein Zone by detecting long branches in phylogenetic data. Molecular Phylogenetics and Evolution 8: 375-384, and outgroup selection issues were discussed in Lyons-Weiler, J., G. A. Hoelzer and R. J. Tausch. 1998. Optimal outgroup analysis. Biological Journal of the Linnean Society 64: 493-511. The programs are available as Macintosh executables from their web page at

There does not seem to be any web site for either this program or its author.

[Tree Gardener icon here] Tiago Ramos of the Museu de Zoologia, Universidade de Sao Paulo, Sao Paulo, Brazil (tcramos  (at) has developed Tree Gardener version 2.2.1, a shell to run Hennig86 interactively on Windows systems. The program allows the user to edit data files, submit jobs, including successive weighting runs, rerooting, and consensus trees. It displays the resulting trees and allows the user to edit them. It is freely available provided that the user has a registered copy of Hennig86. Tree Gardener is available from the Digital Taxonomy web site at

Black is still at Colorado State but seems to have ceased ftp distribution of BIOSYS-2

William C. Black of the Department of Microbiology, Colorado State University (wcb4  (at) ) makes available BIOSYS-2. This is a modified version of David Swofford and Richard B. Selander's 1981 program BIOSYS-1, adding some features. Swofford's program was originally distributed by the Illinois Natural History Survey but has not been in distribution for some years -- this is the only version in distribution. Although in many respects it has been superseded by other population genetics packages (such as the ones that follow this listing) it computes gene frequencies, linkage disequilibria, and many other population genetics analyses on electrophoretic genotypes. For our purposes, it is most relevant to note that it can compute the genetic distances of Nei (unbiased distance), Rogers, and Cavalli-Sforza. It can also carry out UPGMA, WPGMA, Complete Linkage, and Single Linkage clustering of populations (inferrring clocklike phylogenies), or infer nonclocklike phylogenies by Farris's Distance Wagner method. Black has added the capabilities of making bootstrap replicates of the genetic distances and writing them out in PHYLIP format. BIOSYS-2 is available as a DOS executable with documentation and FORTRAN source code. It is distributed by ftp from in directory pub/wcb4.

Rambaut has discontinued distribution of End-Epi, as its features are replaced by the latest versions of Pybus and Rambaut's program Genie

[End-Epi icon here] Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) has written End-Epi (Endemic-Epidemic) version 1.0, a program to examine trees to assess relative cladogenesis (whether there is evidence that one clade has speciated more than another), and make lineages-through-time plots, with the objective of discovering whether the rate of speciation has been constant through time ("endemic") or has been higher initially ("epidemic"). Rambaut considers that the methods in End-Epi have since been superseded by those in his and Oliver Pybus's program Genie. End-Epi is available free for Macintoshes with system 7.0 or later from its Web page at or by ftp from in directory packages as file End-Epi10.hqx. However the Macintosh executable will not work with operating systems later than version 7.5, unless you switch off Modern Memory Manager in the control panel first.

George is still at the University of Michigan but the web page distributing this program has disappeared

George Estabrook of the Department of Biology, University of Michigan, Ann Arbor, Michigan (Estabrook  (at) has written QUARTET2, which calculates measures of difference between phylogenies based on quartets (subtrees of four tips). The methods are described in a paper: Estabrook, G. F. 1992. Evaluating undirected positional congruence of individual taxa between two estimates of the phylogenetic tree for a group of taxa. Systematic Biology 41: 172-177. QUARTET2 is available as a DOS executable from his web page of computer programs at

George is still at the University of Michigan but the web page distributing this program has disappeared

George Estabrook of the Department of Biology of the University of Michigan, Ann Arbor, Michigan (gfred  (at) distributes MEAWILK (MEAcham and WILKinson criteria) which uses a randomization test to evaluates support from character data for hypothesized monophyletic groups It uses criteria published by Christopher Meacham (1994. Phylogenetic relationships at the basal radiation of angiosperms: Further study by probability of character compatibility. Systematic Zoology 19: 506-522) by Mark Wilkinson (1998. Split support and split conflict randomization tests in phylogenetic inference. Systematic Biology 47: 673-695). MEAWILK is a DOS executable distributed from Estabrook's programs web site at

MARKOV seems to no longer be available as a program. A web server service for it was announced, but there is no response when I try it.

The program MARKOV, by Graziano Pesole of the University of Milan (graziano.pesole  (at) and Professor Cecilia Saccone of the University of Bari, Italy, computes a distance measure between pairs of nucleotide sequences. It also constructs phylogenies from these and summarizes the 4x4 substitution matrices between the pairs of species. It uses a more general model of substitution than used in PHYLIP, the Stationary Markov Model published by Lanave et al. in Journal of Molecular Evolution 20: 86-93 in 1984. This is also described in the paper by Saccone et. al. in Methods in Enzymology volume 183, pages 570-583, 1990. It is often known as the General Time Reversible model. Bootstrapping is used to analyze the statistical error of the results. Output files from CLUSTAL and PILEUP, as well as some other formats, can be used for input, and analysis can be confined to certain codon positions in coding sequences. The program is written in ANSI C and runs on Unix systems. A Web page server is also available at

Salisbury says that as he is no longer in academia he no longer has time to distribute this program. His recent email address is b.salisbury  (at)

[SECANT icon] Benjamin Salisbury (ben  (at), of the Department of Ecology and Evolutionary Biology, Yale University has released SECANT version 2.2, based on an earlier program, CLINCH, by Kent Fiala, now of SAS Institute. SECANT was previously known as CLINCH2. It is probably the most sophisticated compatibility analysis (clique analysis) program, capable of handling unordered multiple states. It can also group characters by Salisbury's own Strongest Evidence criterion. It and its criteria are described in a paper: Salisbury, B. A. 1999. Strongest evidence in compatibility: clique and tree evaluation using apparent phylogenetic signal. Taxon 48: 755-766. SECANT is available as a Windows95/NT executable, and its source code is described as available on request. It is available from its web page at

Bailey Kessing has moved to Maryland and for the moment there seems to be no web or ftp distribution of this program

[Sequencer icon here] Bailey Kessing of the Smithsonian Tropical Research Institute, Panama (BaileyKessing  (at) has released Sequencer on 6.1.0, a multipurpose program for manipulating and analysing data. It can calculate many kinds of statistics, but for the purposes of this listing, its important features are the ability to calculate variety of distances from DNA and protein sequence data. Distances for DNA sequence data include Jukes-Cantor, Kimura's 2 parameter model, and computation of synonymous and nonsynonymous substitutions using Kimura's 2 parameter model. It can also bootstrap distance calculations. It is available as Macintosh executables (both PowerPC and non-PowerPC executables are available) from its web site at

Black is still at Colorado State University but seems to have discontinued distribution of this package

William C. Black of the Department of Microbiology, Colorado State University (wcb4  (at) has produced PROGRAMS FOR ANALYSIS OF RAPD-PCR DATA. There are 7 programs. The ones relevant to this listing are

Other programs compute FST and linkage disequilibria from RAPD data. The programs are in FORTRAN source code with DOS executables. They are distributed by ftp from in directory pub/wcb4 as file RAPDS.ZIP.

This program seems to not be distributed any longer. A recent email address for Salisbury is b.salisbury  (at) The Kim lab is now at the University of Pennsylvania but does not have this program available at their web site.

Ben Salisbury (ben  (at) of the Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, has released DNASEP, which uses (with permission) some code from my PHYLIP program DNAPARS to carry out Salisbury's criterion of Strongest Evidence Parsimony. The criterion is described in a paper: Salisbury, B. A. 1999. Strongest evidence: maximum apparent phylogenetic signal as a new cladistic optimality criterion. Cladistics 15: 137-149. DNASEP is available as a Windows95 executable from Salisbury's web site at It has been partially superseded by a later program of Salisbury's, SEPAL, which has more functions.

This program seems to not be distributed any longer. A recent email address for Salisbury is b.salisbury  (at) The Kim lab is now at the University of Pennsylvania but does not have this program available at their web site.

[SEPAL icon] Ben Salisbury (ben  (at) of the Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, has written SEPAL, version 1.01, which can search for the trees that maximize the Strongest Evidence criterion, Apparent Phylogenetic Signal. It can also do Iterative SE, parsimony, and parsimony jackknifing. It can also calculate decay values (Bremer supports) for either parsimony or Strongest Evidence. It also has some options for removing characters that are particularly noisy. The criterion is described in a paper: Salisbury, B. A. 1999. Strongest evidence: maximum apparent phylogenetic signal as a new cladistic optimality criterion. Cladistics 15: 137-149. SEPAL is available as a Windows95 executable from Salisbury's web site at

Belyi is no longer at Penn State and his program is not in distribution. His email address currently seems to be sambauser  (at)

Igor Belyi (Igor_Belyi  (at) has developed TreePack, a minimum evolution program for Unix workstations. TreePack can be obtained by ftp from in directory pub/belyi. It is available as Unix source code in C.

The ftp distribution of QR2 seems to have become nonfunctional. Gascuel is still at this email address, and the Institut Pasteur server for this program is still functional.

Olivier Gascuel and Denise Levy (gascuel  (at) at the the Laboratoire d'Informatique, de Robotique et de Micro-Electronique de Montpellier (LIRMM) of the Universite de Montpellier II, France have produced QR2 version 1.0, a program which approximates a dissimilarity (or distance) matrix by a tree. The method is described in a paper: Gascuel, O. and D. Levy. 1996. A reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance. Journal of Classification 13: 129-155. The program is available in C++ source code by ftp from in directory pub/genome/phylo. It is also available as a server from the Institut Pasteur.

Posada is in Vigo at the email address indicated, but his software site there no longer includes this program.

David Posada (dposada  (at) of the University of Vigo, Spain has produced MATRIX version 1.5, a program to calculate a matrix of pairwise distances (treating gaps as a fifth state by default): for absolute, uncorrected, JC69 and K80 distances from a set of aligned DNA sequences in PHYLIP sequential or NEXUS format. It is available as a Macintosh executable from its web site at

Salminen is currently at the National Public Health Institute in Helsinki, Finland. His email address is mika.salminen  (at), but he does not seem have the Bootscanning Package currently available anywhere.

Mika Salminen and Wayne Cobb (msalminen  (at) and wcobb  (at), of the Henry M. Jackson Foundations for the Advancement of Military Medicine, Walter Reed Army Institite of Research, Bethesda, Maryland, have released the Bootscanning Package, version 1.0beta. This is a series of shell scripts and programs that analyze DNA sequences for evidence of recombination. It breaks the sequence into separate pieces that are analyzed for the bootstrap support of various groups, and it looks for evidence of significant conflict among trees for different parts of the sequence. The programs are currently available only as Sun executables. They require GDE 2.2a and PHYLIP version 3.4 to work. They are available by anonymous ftp from from in directory /hiv/mirrors/pub/programs.

Zharkikh and Rzhetsky are respectively, with Myriad Genetics in Utah, and Columbia University Genome Center. VOSTORG does not seem to be distributed anywhere.

Andrey A. Zharkikh, Andrey Rzhetsky, and co-workers in the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia, have produced VOSTORG, a package of programs for alignment (both manual and automatic) and inferring phylogenies by distance methods and parsimony for molecular sequences. (Zharkikh and Rzhetsky are currently in the US; their e-mail addresses are zharkikh  (at) and andrey  (at) VOSTORG runs on under DOS on PC-compatibles and includes some rather fancy graphics (for DOS). It is available from its Web page in Russia from The programs are described in a paper: Zharkikh, A. A., A-Yu. Rzhetsky, P. S. Morosov, T. L. Sitnikova, and J. S. Krushkal. 1991. VOSTORG: a package of microcomputer programs for sequence analysis and construction of phylogenetic trees. Gene 101: 251-254.

Fitch is still at this address but the programs do not seem to be currently distributed.

Walter Fitch (wfitch  (at), of the Department of Ecology and Evolutionary Biology, of the University of California at Irvine, has available by anonymous ftp at in directory pub/outgoing/evoprog about 20 programs which carry out various kinds of phylogeny estimation and related tasks. They are available in source code in FORTRAN 77, (except for a few which are in C) and also as Sun SPARC executables and as DOS executables. They include:

There are also many programs that convert sequences among various formats, generate all possible trees, shuffle sequences, align sequences, and do various other functions. The programs are available by anonymous ftp from in directory pub/outgoing/evoprog.

There is also TDRAW which draws a tree in Postscript. This program is in C, and is not available as a DOS executable. It is available in directory pub/outgoing/tdraw.

Kay Nieselt-Struwe is currently at the Zentrum für Bioinformatik Tübingen, Germany, but she does not make this program available from there.

Kay Nieselt-Struwe (kns  (at) of the Department of Physics of the University of Auckland, New Zealand has released version 1.0 of STATGEOM. It carries out computation of the statistical geometry in distance and in sequence space of a set of aligned DNA/RNA, amino acid or binary sequences. The user can decide to either compute the overall tree-likeness of the whole set, or a certain subset, or given a tree of the sequences compute the reliability of certain edges in the tree. Postscript files of the graphs of the statistical geometry are automatically generated. A sequence reformatting utility allow various sequence formats to be read in. STATGEOM is written in ANSI C; source code with documentation and a Sun SPARC executable are available by anonymous ftp at (or in directory pub/kniesel. The method of statistical geometry was originally published in: Eigen, M., Winkler-Oswatitsch, R. and Dress, A. 1988. Statistical geometry in sequence space: a method of comparative sequence analysis. Proc. Natl. Acad. Sci. USA 85: 5913-5917.

There is no sign that this program is still available

Hang-Kwang Luh, John Gittleman, and Mark Kot of the University of Tennessee at Knoxville have made available PA, a package of Macintosh programs that implement the phylogenetic autocorrelation comparative method introduced by Gittleman and Kot ( Systematic Zoology , 1990). It is free and is available by anonymous ftp from in directory pub/luh.

Blomberg has moved to Sydney, and I do not know whether this program is currently distributed anywhere.

Simon Blomberg, of the School of Botany and Zoology of the Australian National University, Canberra (S.Blomberg  (at) has announced the beta-release of a small comparative method program, Fels-Rand version 0.91beta [look folks, don't blame me, I had nothing to do with naming this program]. It is designed to analyse data when the phylogeny is only poorly known, as when there is one or several polytomies. The program is said to be inspired by a 1994 paper in Systematic Biology by Jonathan Losos. It retains known tree topology and randomises the unknown parts of the tree, unlike some other programs, which randomize the whole tree. The statistics are calculated on independent contrasts from fully (randomly) resolved trees. Fels-rand is written in XLISP-STAT, and runs in the XLISP-STAT environment (in other words you first must get and install XLISP-STAT on your computer to run the code, which is written in the XLISP-STAT language). XLISP-STAT is available for Macintosh, Windows, and Unix. Fels-rand is available from Blomberg's home page at Its README file can be found in a newsgroup posting at

Dopazo is now at the Centro Nacional de Investigaciones Ocológicas (jdopazo  (at) He appears not to have ABLE in distribution at this time.

Joaquin Dopazo of the R&D Department of TDI (TDI-EMBNet), Spain, (dopazo  (at) has written a program ABLE (Analysis of Branch Length Errors) which implements the method described by Adell and Dopazo in J. Mol. Evol. 38: 305-309 (1994). This is a parametric bootstrap test of constancy in evolutionary rates. The idea of the test is to simulate a large number of a data sets under the model of rate constancy and then to examine the distribution of the branch lengths. After, a tree is reconstructed without the constraint of rate constancy it can be checked whether the observed branch length values fall within the expected distribution. The program is intended for use with the PHYLIP programs FITCH and KITSCH. It is available as a DOS executable from Dopazo's software web page at or by anonymous ftp at: in directory pub/cnb/molevol.

Dopazo is now at the Centro Nacional de Investigaciones Ocológicas (jdopazo  (at) He appears not to have SOTA in distribution at this time. There is a never-completed web page there for it but it is not distributed from that page. A modified version is available for clustering genes for gene expression.

Joaquin Dopazo and J. M. Carazo ( jd19662  (at) and carazo  (at) have produced SOTA, a package to carry out the Self Organizing Tree Algorithm. It is based on Kohonen's unsupervised neural network of self-organizing maps and on Fritzke's growthing cell structures algorithm to construct phylogenetic trees from biological molecular sequence data. It is described in a paper: Dopazo, J. and J. M. Carazo. 1997. Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree. Journal of Molecular Evolution 44a: 226-233. SOTA can use sequence data, distance matrix data, or dipeptide frequencies from proteins. SOTA is available as source code in C for Unix, as executables for SGI workstations, and also with a Windows program called Drawer that draws the resulting trees. The package with documentation is available by anonymous ftp from in directory cnb/sota.

Ken is at the address below but as far as I can tell does not make RSVP available any longer.

Ken Rice (ken_a_rice  (at) of GlaxoSmithKline Beecham, Upper Merion, Pennsylvania (and adjunct faculty at the University of Pennsylvania) has produced RSVP (restriction site variability program) which calculates several measures of genetic variability based on restriction map data. It also produces Jukes-Cantor corrected distance matrices with standard errors from collections of restriction maps. C source code for Version 2.08 of RSVP is available free by anonymous ftp from: in directory pub/rice. It runs under Unix.

Nick Grassly is currently at the Department of Infectious Disease Epidemiology of Imperial College School of Medicine, St. Mary's Campus, London (n.grassly  (at) This program seems not to be currently available there.

[SEQEVOLVE icon here] Nick Grassly (formerly of the Department of Zoology, University of Oxford, most recently of the Department of Biology, Imperial College, London) has written SEQEVOLVE, a program that takes standard (Newick) formatted treefiles and evolves sequences along them following a stochastic process with the expected number and type of substitutions calculated according to a model of molecular evolution. A variety of nucleotide substitution models are implemented: Jukes and Cantor (1969), Kimura (1980), Felsenstein (1981), Hasegawa et al, (1985), and the DNAML model from PHYLIP (Felsenstein, 1995). a PowerMacintosh and Macintosh executable is available, as well as source code files for Unix systems. SEQEVOLVE does not allow for rate heterogeneity among sites or among codon positions as his more recent program Seq-Gen does. SEQEVOLVE is available by ftp from in directory packages/grassly/Seqevolve as files seqevolve-mac.hqx or seqevolve.tar.Z.

John is now at University of California, San Diego, and has not continued to distribute this program.

John Huelsenbeck (johnh  (at) of the Department of Biology of the University of Rochester has written TheSiminator, version 2.0, a program that simulates the evolution of nucleotide sequences along a given tree or trees. It allows for gamma-distributed rate variation among sites, and the Hasegawa-Kishino-Yano 1985 model of nucleotide substitution. It is distributed as C source code and as a Macintosh executable, with examples of input files. It can be fetched from the Huelsenbeck laboratory software web page at (The C source code without the Macintosh executable is also available from the Slatkin Lab's software Web page at

John is now at University of California, San Diego, and has not continued to distribute this program.

[StratCon icon here] John Huelsenbeck (johnh  (at) of the Department of Biology of the University of Rochester has written StratCon, a program to test the consistency of a tree with stratigraphy of the species. It uses a permutation test described in the paper Huelsenbeck, J. 1994. Measuring and testing the fit of the stratigraphic record to phylogenetic trees. Paleobiology 20: 470-483. The program is available as a Macintosh executable. It can be fetched from the Slatkin Lab's software Web page at

Sherbakov seems to be at Irkutsk State University now. I do not know of any distribution of this program.

Dmitri Yu. Sherbakov of the Laboratory of Molecular Systematics, Limnological Institute, Russian Academy of Sciences, Irkutsk (dysh  (at) manually. It gets species names from a sequence file in Sequential PHYLIP format with up tp 150 sequences, then allows you to build multiple trees by clicking on species names. It allows multifurcations. UO is distributed as C sources and Linux binaries from its web page at It requires X windows and the XForms library.

Pagel has subsumed Continuous into the package BayesTraits which he and Andrew Meade have produced. and there is now no separate distribution of Continuous. The web address has also changed -- the new one is available in the listing for that package.

Mark Pagel, of the School of Biological Sciences of the University of Reading, U.K. (m.pagel (at) has written Continuous, version 1. This is a program to fit a generalized least squares (GLS) model to continuous character data on a given tree. The method infers several parameters that allow testing of whether the data shows any phylogenetic signal, and whether change is punctuational. It can also test random walk versus directional change models, and infer ancestrat states. The method is described in two papers:

Continuous is a Mac OS executable. It is downloadable from its web page at

TurboTree seems to have been withdrawn some time ago from the Massey University programs in distribution. Incidentally, it was described in a paper in CABIOS in 1987.

David Penny (Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand) has been offering for free distribution two DOS programs, one a fast parsimony program, TurboTree. There is also another, Great Deluge, an approximate search for the most parsimonious tree by a quasi-random method. He tells me that funding exigiencies are such that he may soon have to start charging for these. His electronic mail address is dpenny  (at)

The CIPRES platform available in this early version has ceased to be distributed, as a newer and more comprehensive platform is under active development.

 The CIPRES project (Cyber Infrastructure for Phylogenetic RESearch), an NSF-funded consortium of many institutions centered on the University of New Mexico, the University of Texas at Austin, and the San Diego Supercomputer Center and coordinated by Bernard Moret (moret  (at), Tandy Warnow (tandy  (at), and Mark Miller (mmiller  (at) has released version of their software platform for analyzing molecular sequences from large numbers of species. This is written in Java and includes a copy of MrBayes. It allows the user to read a data set in NEXUS format, and a provisional tree, and carry out the DCM3 divide-and-conquer algorithm for dividing the data set into overlapping subsets of sequences. Runs of MrBayes on these can then be launched on the same machine or on other machines. The intent is to enable very large data sets of up to 7,000 sequences to be analyzed by combining the results of the MrBayes runs. There is also an intention to soon include support for running PAUP*. The CIPRES software is available for WindowsXP, Mac OS X, and Linux. It can be downloaded from the CIPRES software web page at ttp://

TOPAL versions 1 and 2 have been superseded by TOPALi and they are no longer in distribution.

[TOPAL icon]  Gráinne McGuire, currently of Taylor Fry Consulting Actuaries, Sydney, Australia (grainne  (at) and Frank Wright of Biomathematics and Statistics Scotland, in Dundee (frank  (at), have released TOPAL, which checks for evidence of past recombination events, by looking for changes in the inferred phylogenetic tree TOPology between adjacent regions of a multiple sequence ALignment. Their method detects recombinations by sliding a window along a sequence alignment, and measuring the discrepancy between the trees suggested by the first and second halves of the window, using distance matrix methods. TOPAL version 2 includes a statistical test, based on parametric bootstrapping, and an improved statistic which reduces the effect of among-site rate heterogeneity on the results. The original method is described in the paper: McGuire, G., F. Wright, and M. J. Prentice. 1997. A graphical method for detecting recombination in phylogenetic data sets. Molecular Biology and Evolution 14: 1125-1131. The TOPAL 2.0 program, and recent changes to the method, are described in a paper: McGuire, G. and F. Wright. 2000. TOPAL 2.0 : improved detection of mosaic sequences within multiple alignments. Bioinformatics 16: 130-134. TOPAL is a set of Unix Bourne shell scripts and C code, plus four programs in C from my PHYLIP package. These are available from the TOPAL web site These are available from the TOPAL web site at A Windows interface to TOPAL, written by Iain Milne in Java, called TOPALi, is available at the TOPALi web site at It is described in the paper: 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: 1806-1807.

The homoplasy test software is no longer available -- the web site that distributed it was Maynard Smith's personal web site, and after his death in 2004 that site was finally taken down. Although I do not know of any current distribution, the test itself is implemented in the S.T.A.R.T. package. The web site of recollections of Maynard Smith mentioned below is still available. Noel Smith is at the Centre for the Study of Evolution of the University of Sussex (Noel (at) and also at the Veterinary Laboratories Agency Weybridge. I do not know of any distribution of this program from any web site there. The page of tributes to John Maynard Smith is temporarily down, but Noel Smith hopes to put it back up in the future.

John Maynard Smith and Noel Smith of the School of Biological Sciences of the University of Sussex (noelsmith  (at) released programs to carry out their homoplasy test for recombination in sequences. The test is described in a paper: Maynard Smith, J. and N. H. Smith. 1998. Detecting recombination from gene trees. Molecular Biology and Evolution 15: 590-599. The programs are distributed in QBASIC for DOS and must be run using QBASIC. They are available from Maynard Smith's web site at (John Maynard Smith, a true leader in evolutionary biology, died in April, 2004. Here is a nice page of recollections of him, often amusing, by other biologists. His home page is still available.)

As indicated below, Accelrys, Inc. has discontinued distribution and support for GCG (in spite of a petition from users asking it not to) as of June, 2008

Genetics Computer Group ("GCG"), a subsidiary of Accelrys, Inc., produces the GCG Wisconsin Package, version 10.3, a leading package of sequence search and analysis programs, together with updates of the leading sequence databases. Included are programs for tree-based multiple sequence alignment, calculation of distances, and estimating phylogenies by the neighbor-joining and UPGMA distance matrix methods:

The Wisconsin Package contains front ends in X windows or as a web interface (SeqWeb, sold separately by Accelrys). The GCG Wisconsin Package includes PAUPSearch and PAUPDisplay, which provide a front end to PAUP*. The GCG Wisconsin Package runs on Compaq (Digital) Unix workstations (under Tru64 Unix 4.0E or later), Silicon Graphics workstations (under IRIX 6.5 or later), or on Sun SPARC-based workstations (under Solaris 2.6 or later), IBM AIX systems (version 5.1 or later), or Intel-compatible Red Hat Linux systems (version 7.1 and later). The programs are described on the Accelrys Additional Products web page at There it is announced that distribution and support of the GCG package will cease in June 2008. It is not made clear how to order it before then. Prices are no longer given on the web site (you are asked to contact them). The most recently posted prices (several years ago) were $5,000 (plus $3,000 per year thereafter) for an academic installation ($18,000 and $6,000 for a nonacademic installation). These have probably changed since then.

The Saitou lab in Mishima seems to have removed this program from distribution.

Naruya Saitou of the Laboratory for Evolutionary Genetics, National Institute of Genetics, Japan (nsaitou  (at) has produced TreeTree, a set of programs for neighbor-joining distance matrix analysis with bootstrapping. Macintosh executables are provided, and documentation and Pascal or C source code is provided in the package. The package consists of three main programs: NJ, a standard neighbor-joining program, NJorg, which makes an unrooted neighbor-joining tree, and bootNJ, which bootstraps the analysis, given a data file with multiple distance matrices, one for each bootstrap replicate. It can be downloaded by anonymous ftp from in directory pub/mac/TreeTree.

Jaap Buntjer is still at Keygene, but for a while there was no sign that this program is currently distributed. But now it is available again at and will shortly be back in our listing.

  Jaap Buntjer (jaap.buntjer (at), when he was at the Laboratory of Plant Breeding, Wageningen University, Wageningen, Netherlands wrote Phyltools, which is distributed by the Laboratory. It is a package of utilities for 0/1 binary, interval, and quantitative data (including morphological data, RFLPs, RAPDs, and AFLPs) that can calculate distance matrices, carry out bootstrapping and some permutation methods, and do a number of conversions between different formats. It is intended to work with the PHYLIP package and can read and write PHYLIP file formats. Phyltools is a Windows executable. It can be downloaded from its web site at

This is no longer available, as far as I know. I do not know whether Ken is at the same email address.

Ken Rice (ken_a_rice  (at) of GlaxoSmithKline Beecham, Upper Merion, Pennsylvania (and adjunct faculty at the University of Pennsylvania) has produced AMP (Accepted Mutation Parsimony), a program which calculates stepmatrices for protein parsimony analysis, for use in PAUP* and MacClade. It uses transition probabilities under models of protein evolution to calculate these stepmatrices. It is available as C source code for Unix, from its web site at

This product seems to have been discontinued by BioRad. All that they now have for it is some old manuals, in their Discontinued Software section of their web pages.

BioRad, division of Sadtler USA, Inc., (Sadtler_USA_Sales  (at) distributes Fingerprinting II Informatix Software, a package for quantitative RFLP and Fingerprinting analysis. The package is available for PC and Macintosh, and includes average linkage clustering of the gel patterns. The web page for this software is at (To find the page for the programs you have to choose the links there for "Life Sciences Research", "Software", and then "Fingerprinting II Informatix Software". BioRad's headquarter is at 1000 Alfred Nobel Drive, Hercules, California 94547, and their phone number is (510) 724-7000. Other contact information is available on their web page. One mention of the price elsewhere is that it is from $5,170 up to $20,119.

This program is no longer listed at the Gu lab software site. Gu is still at the address listed and distributes other programs at that site.

Xun Gu, of the Department of Genetics, Development and Cell Biology and the Center for Bioinformatics and Biological Statistics atIowa State University, Ames, Iowa (xgu  (at) together with Wei Huang, Dongping Xu, and Hongmei Zhang has produced GeneContent, version 1.0.2, a program to compute distances between whole genomes from their gene contents. It uses the presences and absences of gene families (or an extended version which also notes the presence of a gene family only as a single copy). It also uses these distances to compute a Neighbor-Joining tree of genomes. It is described in a paper: Gu, X., W. Huang, D. Xu, and H. Zhang. 2005. GeneContent: software for whole-genome phylogenetic analysis. Bioinformatics 21: 1713-1714.

Jermiin is at the University of Sydney, and at the University of Rome "Tor Vergata" as well right now. The link for this program at his software page in Sydney seems to be broken, for now.

Lars Jermiin of the School of Biological Sciences of the University of Sydney, Australia (lars.jermiin  (at) and Olena Anpilogova have produced TreeCons version 1.0. It generates a weighted consensus tree from trees obtained by maximum likelihood analysis, generates relative likelihood support on edges in this and other user-specified trees, and does the Kishino-Hasegawa test with any level of significance. It reads output files and tree files produced by some of the programs in PHYLIP, MOLPHY, fastDNAml and TrExMl. The output file from TreeCons is in a format that then is fed back into PHYLIP's program Consense. A number of weighting schemes to compute tree weights from their likelihoods are allowed. The weighting schemes and the underlying theory are described in a paper: Jermiin L. S., G. J. Olsen, K. L. Mengersen, and S. Easteal. 1997. Majority-rule consensus of phylogenetic trees obtained by maximum likelihood analysis. Molecular Biology and Evolution 14: 1296-1302. TreeCons is distributed as C source code. It is available, with documentation and sample input and output, from its web site at

Marty Wolf is still at the same address, but TrExML no longer seems to be distributed.

Marty J. Wolf of Bemidji State University, Minnesota (mjwolf  (at) has written, and he and Lars Sommer Jermiin distribute, TrExMl, which searches tree space for DNA sequence data to find not only the maximum likelihood tree but also trees of other topologies which are nearly as good. TrExMl can also carry out bootstrapping of the sequences before doing the analysis. It is described in a paper: Wolf M. J., S. Easteal, M. Kahn, B. D. McKay, and L. S. Jermiin. 2000. TrExML: A maximum likelihood program for extensive tree-space exploration. Bioinformatics 16: 383-394. TrExMl is described in its web page at It is distributed from there as C source code. One use will be along with Lars Sommer Jermiin's program TreeCons which computes a weighted average of trees according to their likelihood values.

Accelrys Inc. now does not offer DS Gene for sale, but instead points to other of its products that contain analogous features.

Accelrys, Inc., 10188 Telesis Court, Suite 100, San Diego, California 92121, USA (Phone: +1 858 799 5000, Fax: +1 858 799 5100) sells Accelrys Gene version 1.5, a sequence analysis package for Windows with the same functionality as the Macintosh package (formerly owned by them) MacVector. It can do sequence search, alignment using ClustalW, and UPGMA or Neighbor-Joining distance matrix methods with a variety of distance measures and with bootstrap analysis available. It also has many other features including primer design, gene finding, motif searching, protein secondary structure and hydrophobicity prediction, and prediction of restriction digests. It runs on Windows systems and is mentioned on the web page on legacy products at It cannot be ordered through that web page, but one could contact the company and ask how to order it. It is described as "no longer being developed as a stand-alone product", and its functionality is described as being incorporated into two other Accelrys products. However neither of these is described as having the above phylogeny functions. The last time I knew the price, its price for academic use was $2,500, and for commercial use $5,000.

Lars Jermiin has moved on to the CSIRO. This program is not one of the ones in distribution at his software web site, which is currently still at the University of Sydney.

Lars Sommer Jermiin of the School of Biological Sciences of the University of Sydney, Australia (lars.jermiin  (at) (formerly of the John Curtin School of Medical Research of the University of Canberra, Australia) has released K2WuLi version 1.0, a program to calculate the Kimura 2-parameter distance among DNA sequences, to compute its standard deviation, to carry out the relative rate test of Wu and Li (Wu, C.-I. and W.-H. Li. 1985. Evidence for higher rates of nucleotide substitution in rodents than in man. Proceedings of the National Academy of Sciences, USA 82: 1741-1745) , in the form suggested by Muse and Weir (Muse, S. W. and B. S. Weir. 1992. Testing for equality of evolutionary rates. Genetics 132: 269-276). The program is available as a DOS executable with Turbo Pascal course code as well from its web page at

Clare Constantine is now at the University of Melbourne's School of Population Health, but there is no sign of distribution of GeneStrut there or anywhere else.

Clare Constantine of the Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia (constantine  (at) and colleagues at the Division of Veterinary and Biomedical Sciences at Murdoch University, Perth, Australia have written GeneStrut, a Macintosh program which computes a range of standard measures for the analysis of genetic structure from discrete genetic data. The input data are multilocus genotypes. It can calculate genotypic and allelic frequencies, statistics for Hardy-Weinberg disequilibrium, genetic diversity within populations, genetic identities between populations, and indices of population structure (F-statistics). For our purposes the important feature is that it can also calculate Nei's genetic distance between populations, with standard deviations. It is described in the paper: Constantine C. C., R. P. Hobbs and A. J. Lymbery. 1994. FORTRAN programs for analysing population structure from multilocus genotype data. Journal of Heredity 85: 336-337. It is available as a Macintosh executable, at its web site at

This seems to no longer be available at the Pasteur Institute sites

Denis Beaumont (beaumont  (at) has made a parallelized version of fastDNAml called VeryfastDNAml. It is parallelized with the TreadMarks distributed shared memory system, which is a not-quite-free environment for parallelization that runs on many workstation-class machines. The C source code of VeryfastDNAml is available by ftp from the Institut Pasteur server in directory /pub/GenSoft/unix/evolution/FastDNAml as file fastDNAml-tmk.tar.gz. There is a web page access to this ftp distribution at, which includes a link to the TreadMarks project.

This does not seem to be in distribution anywhere now. Hoffmann is at Texas A&M University now. Opazo is at the Instituto Ecologia y Evolución of the Universidad Austral de Chile. His email address is jopazo (at)

Federico Hoffmann and Juan Opazo of the School of Biological Sciences of the University of Nebraska, Lincoln, Nebraska (federico (at) and jopazo (at) have written Codeml3X, a script that runs Codeml three times. It runs CODEML from PAML three times in a row, with three different starting omega values. The script will create a directory and three subdirectories where the results of each run will be saved, and it will also create a text file with the likelihood scores of each tree for each run. It is available as Perl script. It can be downloaded from its web site at

Hadtree, Prepare, and Trees seem not to be distributed from Penny's web site (or anywhere else). Penny continues to be at Massey University.

David Penny of the Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand (dpenny  (at), has made available through his Farside Institute three programs, Hadtree, Prepare, and Trees. These run on DOS systems, and compute bipartition spectra by Hadamard transformations (conjugations and the distance Hadamard), character weighting, distance transformations (including LogDet), base composition tests, resampling schemes, and tree selection. The programs are available from the Farside Institute downloads page at

I cannot locate Jakobsen or find any evidence that this program is still in distribution.

Ingrid Jakobsen (currently of the Advanced Computational Modelling Centre, University of Queensland, Australia, ibj  (at) and Simon Easteal of Australian National University, Canberra, have released reticulate. It is a compatibility matrix program for DNA sequences that has features designed to test for evidence of reticulate evolution (such as recombination). The program computes and displays a pairwise compatibility matrix for all pairs of sites. It can randomize the order of sites and compute the fraction of compatible sites in a region for the randomizations, to test whether there is a pattern suggesting reticulation. The program is distributed as C source code for Unix and X Windows, though there are some limited ways of running it without X Windows. It is described in the paper: Jakobsen, I. B. and S. Easteal. 1996. A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. CABIOS 12: 291-295. It is available from Ingrid Jakobsen's software web site at

Andrew is now at the University of Edinburgh. His software site there no longer distributes LARD

[LARD icon here] Andrew Rambaut of the Department of Zoology, University of Oxford, England (andrew.rambaut  (at) has produced LARD (Likelihood Analysis of Recombination in DNA) version 2.2, a program to detect the presence of recombination in a set of sequences. LARD looks at the set of sequences to discover which are the most plausible parents of a potentially recombinant sequence, and performs a likelihood ratio test for each possible breakpoint position of whether the three-species tree differs on the two sides of the breakpoint. LARD is described as an extension of a method suggested by John Maynard Smith: Maynard Smith, J. 1992. Analysing the mosaic structure of genes. Journal of Molecular Evolution 34: 126-129. It is described in a paper: Holmes, E. C., M. Worobey, and A. Rambaut. 1999. Phylogenetic evidence for recombination in dengue virus. Molecular Biology and Evolution 16: 405-409. LARD is available as C source code and as a Macintosh executable from its web site at

The Mark Gibbs / Adrian Gibbs lab is still around (their web site is here) but they seem not to distribute SiScan any more

Adrian Gibbs (Adrian.Gibbs  (at) of the Department of Botany and Zoology of the Australian National University, Canberra, has written SiScan, version 2.0, a program that scans 3 or 4 DNA sequences for evidence of recombination. Two of the sequences are the putative parent sequences, one the putative recombinant, and one an outgroup. The program uses a Monte Carlo randomization procedure to test for recombination signal. The program can be downloaded as an archived Windows executable (that's what I assume it is, the web site doesn't say) from the department software distribution web site at SiScan is described in a paper: Gibbs, M. J., J. S. Armstrong, and A. J. Gibbs. 2000. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.

This program does not seem to be currently distributed either at Worobey's department (Ecology and Evolutionary Biology at the University of Arizona), or Rambaut's department (the Institute of Evolution at the University of Edinburgh, U.K.).

[PIST icon] Michael Worobey, of the Department of Ecology and Evolution, University of Arizona, Tucson, Arizona (worobey  (at) and Andrew Rambaut, of the Department of Zoology, University of Oxford (andrew.rambaut  (at) have written PIST (Phylogenetic Informative Sites Test) version 1.0, a program to perform this test. The program simulates multiple data sets up a given tree, and then computes, for each of these and for an original data set, a statistic which is the proportion of sites that have two states and fit the tree perfectly. This statistic will be inflated in the original data if there are recombination events in its genealogy. The program is available as a Mac OS executable and as source code for Unix (which can also be compiled on Windows or on Mac OS X). It is distributed from its web page at

The website is still there, but currently the download is listed as “unavailable at this time”.

Jonathan Moore and Robin Allaby of the Warwick HRI at the University of Warwick, UK (jonathan.moore (at) has released TreeMos version 1.0, a package for search and visualisation of phylogenetic mosaicism, which identifies anomalous nearest-neighbour relationships of segments in multiple multiple alignments. It allows the user to search for phylogenetic mosaicism in a group of DNA or protein sequence multiple alignments or genome sequences. TreeMos uses a sliding window and local alignment and tree-building algorithms (ClustalW) to identify sequence segments whose nearest neighbour is anomalous to that identified using the whole alignment, and visualizes that relationship where the anomalous neighbour may come from anywhere in the data set. TreeMos can import a group of alignments in FASTA format, identify instances of phylogentic mosaicism within and between alignments, and display graphical representations of the results in a web browser. The methods are described in the paper: Allaby, R.G. and M. Woodwark. 2007. Phylogenetic analysis reveals extensive phylogenetic mosaicism in the Human GPCR superfamily. Evolutionary Bioinformatics 3: 155-168. It is available as a Perl script and Intel Mac OS X executables. It can be run as a command line program, but also requires a local Apache installation for its GUI functionc. TreeMos can be downloaded from its web site at

This program seems mostly to have been superseded by Nielsen and Jody Hey's later programs IMA and IMa2 and it is not currently in distribution. Nielsen is now in the Department of Integrative Biology at the University of California, Berkeley.

Rasmus Nielsen, of the Bionformatics Centre at the University of Copenhagen, Denmark (rasmus (at) has written MDIV, a program that will simultaneously estimate the divergence time and the migration rates between two populations. It can use either an infinite-sites model or an HKY sequence evolution model. It can test whether the evidence supports historical divergence, migration between the populations, or both, and make maximum likelihood estimates and likelihood surfaces for the parameters. It assumes equal population sizes in the two populations and in their ancestors. It is decsribed in a paper: Nielsen, R. and J. W. Wakeley. 2001. Distinguishing migration from isolation: an MCMC approach. Genetics 158: 885-896. It is distributed as a Windows executable from Nielsen's programs web site at

Johan Nylander's website is now here but he is not distributing MCS currently.

Johan Nylander (Johan.Nylander  (at) has written MCS version 1.0, a program that reads the output of boostrap or jackknife analyses in PAUP* and computes the Mean Character Support statistic from them. It is available as a Windows or Mac OS X executable or as source code from Nylander's software download site at Sweden

McInerney is still in Maynooth but is no longer distributing this program, probably because programs like PAML can now bootstrap. And why did I write that this "allows bootstrapping within PAML", when it actually used MOLPHY?

James McInerney of the Department of Biology of the National University of Ireland, Maynooth, County Kildare, Ireland (james.o.mcinerney  (at) and also of the Department of Zoology of the Natural History Museum, London, U.K. (j.mcinerney  (at) has written PHYCON, a program which takes as input bootstrapped molecular data sets, as produced by PHYLIP and feeds them to MOLPHY programs. This allows bootstrapping within PAML. The program is available as C source code for Unix; it will not work on a Windows system or under Mac OS (though it can under Mac OS X). Source code and documentation are available from its web site at

Dopazo is now the head of the department of Bioinformatics and Genomics at the Centro de Investigación Príncipe Felipe in Valencia, Spain. He does not seem to have WET available for distribution.

[WET icon] Joaquin Dopazo of the Bioinformatics department of GlaxoWellcome SA, Spain (jd19662  (at) has written WET (Windows Easy Tree), version 1.3, which is an easy-to-use program for inferring phylogenies from sequence data by distance matrix methods. The main goal in the development of WET was to make a really user friendly program able to interact with other phylogenetic packages. WET can import files of a number of different formats. It calculates distances by a number of different methods and constructs phylogenetic trees using neighbor-joining, UPGMA and WPGMA procedures. It is a Windows executable. It is available from its web site at

Jiang is still at the same address but does not seem to distribute TAAR from there. He has a link to the old TAAR distribution (at McMaster University) but it is not available there.

Feng Liu and Tao Jiang (currently of the Department of Computer Science and Engineering at the University of California, Riverside, jiang  (at), have written TAAR (Tree Alignment And Reconstruction), version 1.0, which constructs multiple sequence alignment and phylogenies based on the idea of tree alignment. It is a graphical environment capable of "approximately optimal" parsimony-based tree alignment. It can also infer trees by parsimony. It can handle DNA or protein data. It is available as C source code for Unix with X Windows (X11R5) and MOTIF 1.2. It is also available in a version for Linux with Lesstif. These are distributed through its home page at

David States is currently in the Brown Foundation Institute of Molecular Medicine at the University of Texas at Houston, but CTREE seems not to be in distribution there.

David States (dstates  (at) of the Department of Human Genetics and Bioinformatics at the University of Michigan, Ann Arbor, Michigan has released Ctree version 1.0., a tree alignment program that uses a Hidden Markov Model method of representing the ambiguities in alignments of groups of sequences. The Ctree program is based on a neighbor joining algorithm in which sequences and groups of sequences are represented by Hidden Markov Models. HMMs are aligned using a Smith/Waterman dynamic programming algorithm to find the best local alignment. At each step in building the MSA alignment tree, the highest scoring pair of HMMs are merged into a new HMM. In this sense it is similar to the progressive alignment algorithm used in ClustalW, but the use of an HMM to represent clusters retains more information about the ambiguities than the Clustal algorithm does. It is possible to write the tree to a dendrogram output file.

Ctree is available by anonymous ftp from in directory pub/ctree. It is available as C source code and also as executables for Sun Solaris, SGI, Linux, and Windows (in version 1.1). Ctree is also useable as a server but that version seems not to give trees as output.

(Sukumaran has apparently withdrawn bootscore. He says that his program SumTrees, which is part of his DendroPy Python package, is its replacement.) of the

Jeet Sukumaran of the Division of Herpetology of the University of Kansas Natural History Museum and Biodiversity Research Center at the University of Kansas, Lawrence, Kansas (jeetsukumaran (at) distributes bootscore version 3.11, a program to compute bootstrap support from boostrap replicate trees and place them on a consensus tree. A platform-independent Python script maps non-parametric bootstrap support for clades onto a phylogenetic tree. It outputs a NEXUS/Newick treefile with the topology of the given tree and with clade support indicated by node labels or branch lengths. In its default bipartition-counting mode, it identifies all distinct bipartitions in the tree to be evaluated, and then scans through a file of bootstrap replicates to identify the percentage or proportional frequency of occurance of each of those bipartitions in each of the bootstrap trees. It can also operate in a clade-counting mode, in which it identifies all distinct monophyletic groups in the tree being assessed, and then counts the number of bootstrap trees in which that particular monophyletic group is recovered. It is available as a Python script. It can be downloaded from its web site at

Purvis is still in the same location, but there seems to be no distribution of this helper application currently.

Andrew Purvis's laboratory of the Department of Biological Sciences at Imperial College, Silwood Park, U.K. (a.purvis (at) have produced Ultrametric Check, a utility to check the clockness of a tree. It calculates the total root-to-tip distance for all tips in a phylogeny. It reads CAIC format .Phyl and .Blen files and works out whether the tips line up (whether the tree is ultrametric). It is available as Mac OS 9 executables. It can be downloaded from its web site at

Neither Emília Martins nor Ted Garland currently distributes CMAP.

Emília Martins (emartins  (at), of the Department of Biology of the University of Indiana, Bloomington, Indiana, has written CMAP, the Comparative Method Analysis Package, for comparative methods analysis. This package was developed when she and Ted Garland were conducting the simulation study described in the paper: Martins, E. P. and T. Garland, Jr. 1991. Phylogenetic analyses of the correlated evolution of continuous characters: a simulation study. Evolution 45: 534-557. It can be used to estimate the correlation between two continuous characters measured in different species while taking phylogenetic information into account. Methods for doing so include several versions of Felsenstein's (1985) independent contrasts, and the sum-of-squared-changes parsimony algorithm. The programs in CMAP are described by Martins as "slow" and "unfriendly". The executables are available only for DOS machines. She is no longer developing this package, and is now concentrating her efforts on her other package COMPARE, which will be able to do everything that CMAP can. CMAP is available from its download area at

Lindenfors no longer distributes CoSta.

[CoSta icon here] Patrik Lindenfors (Patrik.Lindenfors  (at), of the Department of Zoology, Stockholm University Sweden, and the Department of Biology, University of Virginia, Charlottesville (Patrik.Lindenfors  (at), has written CoSta version 1.03, a DOS program which carries out the Contingent States Test for the correlation of changes in two characters along a tree, which is described in the paper: Sillén-Tullberg, B. 1993. The effect of biased inclusion of taxa on the correlation between discrete characters in phylogenetic trees. Evolution 47: 1182-1191. The program reads MacClade data files, and also text files saved from MacClade. The program can be fetched at its Web site at

ACAP 2 seems to have been withdrawn by the Ackerley Lab (he is now at University of California, Berkeley) as its features are available in a more recent package, Cactus-Pie

David Ackerly (dackerly  (at) of the Department of Biological Sciences, Stanford University, Stanford, California has released ACAP 2 (Another Comparative Analysis Program) to carry out independent contrasts methods for comparative analysis. It also also incorporates linear parsimony methods into the program, in order to calculate consistency indices for continuous characters. The program is written in Think Pascal for Macintosh Mac OS systems, and is available from its web site at as a Macintosh executable which will run on 68k Macintosh or PowerMacintosh Mac OS computers.

The Digital Taxonomy listing has disappeared, and with it the last place that CLINCH could be downloaded. Kent Fiala works for SAS Institute and can be reached by email at fiala (at)

Kent Fiala (fiala  (at) (most recently of SAS Institute) produced CLINCH (CLadistic INference by Compatibility of Hypothesized characters) version 6.2. It is a general-purpose compatibility program capable of handling multiple unordered states. It is available as a DOS executable, including FORTRAN source code, from the Digital Taxonomy web page at

Nilsson is in Gothenburg and Ursing is now working for an investment company. galaxie does not seem to be in distribution.

Henrik Nilsson and Bjørn Ursing of the Botanical Institute at the Gøteborg University and the Center for Genomics and Bioinformatics at the Karolinska Institute, Stockholm, Sweden (henrik.nilsson (at) and bjorn.ursing (at) have produced galaxie, a a package of CGI scripts for sequence identification through automated phylogenetic analysis. galaxie is a server, but also makes its scripts available for download. It is intended for identification of fungal EST sequences. It uses BLAST, ClustalW and PHYLIP to find a set of best matches to the EST sequence, then make a phylogeny of these matches and the original sequence to help identify the sequence. The CGI scripts require that the user who installs them be familiar with such scripts and have a web server, a and also have BLAST, ClustalW and PHYLIP installed on their computer. It is described in the paper: Nilsson, R. H., K.-B. Larsson, B. M. Ursing. 2004. galaxie - a CGI script package for sequence identification through automated phylogenetic analysis. Bioinformatics 20: 1447-1452. It is available as a package of Perl scripts. It can be downloaded from its web site at

Rambaut is now at the Institute of Evolutionary Biology at the University of Edinburgh. Bi-De seems not to be still in distribution, probably because he considers his more recent program Phyl-O-Gen to supersede it.

[Bi-De icon here]  Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) has written Bi-De version 0.1, to simulate the evolution of trees using various models of lineage birth and death, and sampling lineages from among those extant. It can simulate branching with or without regulation of the number of lineages. It also allows the user to specify the relationship between the number of lineages and the birth rate of lineages. The program is available free for MacOS system 7.0 or later, from its web page at the University of Oxford Zoology software site at Its manual can also be viewed on-line at that site. Rambaut says that Bi-De is considered obsolete software, having been almost completely superseded by their later program Phyl-O-Gen.

Jermiin is at this place. The web page for Hetero does exist in this location but the download links are not functional.

Lars Jermiin of CSIRO Entomology, Black Mountain Laboratories, Canberra, Australia (lars.jermiin  (at) wrote (when he was at the University of Sydney) Hetero, version 1.0, a program to simulate evolution of DNA sequences on four-species trees. The program allows many different kinds of heterogeneity of processes and rates, including different models of change on different branches. It gives a number of different kinds of summaries of the properties of the resulting sequences, as well as writing them to files for use by other programs. It is described in a paper: Jermiin, L. S., S. Y. W. Ho, F. Ababneh, J. Robinson, and A. W. D. Larkum. 2003. Hetero: a program to simulate the evolution of DNA on a four-taxon tree. Applied Bioinformatics 2: 159-163. It is distributed as executables for Sun Solaris, for Windows, and for Mac OS X from its web site at Source code is also offered to those users who obtain a license for use of source code from the book Numerical Recipes.

... and indeed, Diversi has been superseded by a comparable function within APE, as Paradis promised.

Emmanuel Paradis (paradis (at), of the Institut de recherche pour le développement, Marseille, France has released Diversi version 0.20.0, a program for the analysis of diversification using phylogenetic data. It uses several methods to estimate and test for variations in diversification rates using phylogenetic data, including tests for temporal or among-clade variations in diversification rates using a maximum likelihood method. The program takes divergence times as its input. It can also simulate the branching of trees. he tests are described in a paper: Paradis, E. 1997. Assessing temporal variations in diversification rates from phylogenies: estimation and hypothesis testing. Proceedings of the Royal Society of London B 264: 1141-1147. It is available as FORTRAN source code and also as a Windows executable, from Paradis's software web page at or by ftp from in directory /pub/pc/Log-manu. Paradis describes DIVERSI as no longer developed or maintained, and soon to be superseded by his later program APE.

Opazo is at the Instituto Ecologia y Evolución of the Universidad Austral de Chile. His email address is jopazo (at) Biokubuntu seems to have disappeared, and with it the software distribution.

Juan Opazo of the School of Biological Sciences of the University of Nebraska, Lincoln, Nebraska (jopazo (at) has written MULTIDIVTIME HELPER, a Perl script to create a tree file for constraints for use by Multidivtime. It is designed to facilitate the estimation of divergence times using Multidivtime. This script will create a directory and three subdirectories where the results of each program (baseml, estbranches and multidivtime) will be saved, and it will also create a tree file with node labels to assign constraints, this file has been designed to be opened in TreeView. The script needs baseml, paml2modelinf, estbNew, and Multidivtime to run. It is available as Perl script. It can be downloaded from its web site at

Andrew Rambaut is now at the University of Edinburgh. He has ceased distribution of Rhino.

[Rhino icon]  Andrew Rambaut, of the Department of Zoology, University of Oxford (andrew.rambaut  (at) has released Rhino version 1.2. The program uses nucleotide sequences or protein sequences and a given estimate of the tree, and fits a wide variety of models of sequence evolution. These include DNA, amino acid, and codon models, as well as versions of these with nodes of known time, serial samples, molecular clocks, and relaxed molecular clocks. It is available as a Mac OS X or Mac OS 9 executable, and as source code for Unix (which can also be compiled to work on Windows or Mac OS X). It is available at its web page at

(Frederik Decoutterre may still be with Genohm but there is no sign there that this is one of their products, and the TreeIllustrator web site is gone, replaced by a spam fake web site).

[TreeIllustrator icon]   Frederik Decouttere of Genohm, a spin-off of the University of Ghent in Belgium (Department of Molecular Biology) (info (at) has released TreeIllustrator version 1.6, a program for displaying and manipulating phylogenetic trees. It allows you to customise your phylogenetic trees and compare them with the current classification of organisms. It can import NEXUS and Newick tree files, including multiple trees. Nodes can be dragged with the mouse, names changed, graphical properties of the image can be changed, the root can be changed, and subtrees extracted. There is a browser which accesses the Tree Of Life and can point out inconsistencies between your tree and that one. It is described in the paper: Trooskens, G., D. De Beule, F. Decouttere, and W. Van Criekinge 2005. Phylogenetic trees: visualizing, customizing and detecting incongruence. Bioinformatics 21(19): 3801-3802. It is available as Java executables. There is a free Standard Edition which can handle up to 100 tips, a more capable commercial Enterprise Edition, which can handle very large trees, and is available at a price of 240 Euros from Genohm. It is described at the Genohm web site at, and the Standard Edition can be downloaded from its web site at

This package seems to no longer be downloadable. All that is available at the CEH GeneSwytch site is the web server version.

Paul Swift and Dawn Field of the Centre for Ecology and Hydrology, Oxford, U.K. (pswi (at) have released RPT (Rosette Plotter Tool), version 2.01, that permits visual comparison of multiple continuous characteristics. The Rosette Plotter Tool reads the tree and produces circular plots ("rosettes") which combine relational data with multiple descriptive datasets for ready comparison. The data can be taxonomic, phylogenetic or categorical (eg. habitat type). Descriptive data can be discrete or continuous, and are displayed as relative frequencies. The program accepts NEXUS, PHYLIP and CLUSTAL trees. It accepts datasets describing over 2000 items with up to 20 measured characters. It is available as a Perl script. It can be downloaded from its web site at It is also available as a web server.

Defunct web servers

The following servers have disappeared:

  • PhyloBuilder web server searches for database matches to a seed sequence, aligns the sequences, and builds a neighbor-joining tree and a multiple alignment.
  • TreeNotator server finds and adds Genbank and protein IDs to a tree.
  • The server is no longer available, although the Java programs are still distributed -- see the listing mentioned belowA web server for Phylap a Java applet that generates a random tree, a distance matrix for it, and uses clustering methods to estimate and display the resulting tree and the true one. From David Joyce of the Computer Science Department at Clark University, Worcester, Massachusetts.

    Defunct ftp archives of programs

    Dan was afterwards at Bristol-Meyers-Squibb parmaceuticals (ddavison  (at)

    The Houston ftp archive maintained by Dan Davison at the University of Houston ( seems to have become inactive.

    The mirrors of the IUBIO ftp archive formerly kept in these places seem to have disappeared:

    A mirror of the molbio section is maintained at
    A mirror of the molbio section is available at in directory /pub/mirror_sites/iubio/
    A mirror of the molbio section is maintained at at pub/mirror/molbio
    A mirror of the search, unix, ibmpc, mac, and vax subdirectories of the molbio section is maintained at in directory pub/software

    Defunct lists of phylogeny programs
    (ones no longer distributed)

    Here are some now-defunct entries from my list of other lists of phylogeny programs:

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