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.

Dan is now at Bristol-Meyers-Squibb parmaceuticals (ddavison  (at) timelord.wfd.pri.bms.com)

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

(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.)

Mauro J. Cavalcanti (maurobio  (at) geocities.com), 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 http://www.geocities.com/RainForest/Vines/8695/software.html#Cladistics .

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Kevin Nixon has withdrawn ClaDOS: it is replaced by his more recent program WINCLADA which incorporates the features of ClaDOS and of another program, DADA.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

Andrey Zharkikh (zharkikh  (at) hgc6.sph.uth.tmc.edu ), (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

• Translating, reformatting and printing aligned sequences
• Calculation of evolutionary distances among sequences
• Inferring phylogenetic trees and bootstrapping, by parsimony or neighbor-joining distance methods
• Drawing the tree structure to a PostScript printer

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

James Lake (lake  (at) uclaue.mbi.ucla.edu) 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 http://sinca.fqs.co.jp/InfoSINCA/. 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).

Arnold G. Kluge (akluge  (at) umich.edu), 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 http://www.ummz.lsa.umich.edu/herps/systack.html to download it.

Perhaps this one has expired because Michael Schoeniger is no longer working there.

Johannes Schaefer and Michael Schoeniger of the Lehrstuhl für Theoretische Chemie of the Technische Universität München (schaefer  (at) theochem.tu-muenchen.de and schoeniger  (at) theochem.tu-muenchen.de) have written DISTREE. It computes pairwise distances (substitution rates) of aligned nucleotide sequences utilizing various models of base substitution. Moreover it provides the user with information on the goodness of fit of the models to the given set of sequence data. Each of the models is implemented in two variants, assuming identical and gamma distributed substitution rates across sequence sites. It is available as a DOS executable with C source code, or as source code for Unix systems. DISTREE is distributed through its Web page at http://evol10.theochem.tu-muenchen.de/pub,

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) auckland.ac.nz) 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 http://www.cebl.auckland.ac.nz/"> 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*.

Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) zoo.ox.ac.uk) and Nick Grassly, currently of the Zoologisches Institut, Universität München (grassly  (at) zi.biologie.uni-muenchen.de), 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 http://evolve.zoo.ox.ac.uk/Spot/Spot.html.

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

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 http://bio.uml.edu/LW/RASA.html.

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

Tiago Ramos of the Museu de Zoologia, Universidade de Sao Paulo, Sao Paulo, Brazil (tcramos  (at) ibm.net) 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 http://www.geocities.com/RainForest/Vines/8695/software.html#Cladistics.

William C. Black of the Department of Microbiology, Colorado State University (wcb4  (at) lamar.colostate.edu ) 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 lamar.colostate.edu in directory pub/wcb4.

Andrew Rambaut of the Department of Zoology, University of Oxford, (andrew.rambaut  (at) zoo.ox.ac.uk) 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 http://evolve.zoo.ox.ac.uk/software/End-Epi/End-Epi.html or by ftp from evolve.zoo.ox.ac.uk 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) umich.edu) 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 http://www-personal.umich.edu/~gfred/.

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) umich.edu) 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 http://www-personal.umich.edu/~gfred/.

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) unimi.it) 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 http://bigarea.area.ba.cnr.it:8000/EmbIT/coda_markov.html.

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) genaissance.com

Benjamin Salisbury (ben  (at) aya.yale.edu), 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 http://jkim.eeb.yale.edu/salisbur/.

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

Bailey Kessing of the Smithsonian Tropical Research Institute, Panama (BaileyKessing  (at) email.com) 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 http://nmg.si.edu/Sequencer.html.

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) lamar.colostate.edu) has produced PROGRAMS FOR ANALYSIS OF RAPD-PCR DATA. There are 7 programs. The ones relevant to this listing are

• RAPDPLOT which computes distances between RAPD patterns using either Nei and Li's distance or a percent difference score,
• RAPDBOOT which makes these distance matrices in while bootstrap sampling the data set, and
• RAPDBIOS which converts the RAPD data into a gene frequency dataset for analysis by BIOSYS-2. (Black's site is also the distribution site for BIOSYS-2).

This program seems to not be distributed any longer. A recent email address for Salisbury is b.salisbury  (at) genaissance.com. 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) aya.yale.edu) 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 http://jkim.eeb.yale.edu/salisbur/. It has been partially superseded by a later program of Salisbury's, SEPAL, which has more functions.

Ben Salisbury (ben  (at) aya.yale.edu) 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 http://jkim.eeb.yale.edu/salisbur/.

Belyi is no longer at Penn State and his program is not in distribution. His email address currently seems to be sambauser  (at) katehok.ac93.org.

Igor Belyi (Igor_Belyi  (at) transarc.com) has developed TreePack, a minimum evolution program for Unix workstations. TreePack can be obtained by ftp from ftp.cse.psu.edu 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) lirmm.fr) 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 lirmm.lirmm.fr 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) uvigo.es) 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 http://bioag.byu.edu/zoology/crandall_lab/programs.htm.

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

Mika Salminen and Wayne Cobb (msalminen  (at) hiv.hjf.org and wcobb  (at)  reed.hjf.org), 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 http://www.ktl.fi 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) myriad.com and andrey  (at)  genome2.cpmc.columbia.edu). 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 http://molevol.bionet.nsc.ru/vs.htm. 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) uci.edu), of the Department of Ecology and Evolutionary Biology, of the University of California at Irvine, has available by anonymous ftp at daedalus.bio.uci.edu 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:

• ANCESTOR which searches for most parsimonious trees for nucleotide or protein sequences,
• EVOLVES which carries out the original Fitch-Margoliash distance matrix method,
• WTDPARS, programs for weighted parsimony analysis according to the methods he has introduced in the papers by P. L. Williams and W. M. Fitch, in pages 453-470 of the Nobel Symposium on the Heirarchy of Life, edited by B. Fernholm, K. Bremer, and H. Jornval, Elsevier, 1989, and the paper by P. L. Williams and W. M. Fitch, in Advances in Enzymology, volume 183, pages 615-625, 1990.

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) phy.auckland.ac.nz) 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 cage.mpibpc.gwdg.de (or 134.76.209.64) 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.

Freqpars is described as available on the "Companion Applications" at the PAUP* site (http://paup.csit.fsu.edu/nlinks.html) but the download link for freqpars there does not work. (Also, they spell my name wrong on that page).

David Swofford, of the Laboratory of Molecular Systematics of the Smithsonian Institution, Washington, D.C., has written Freqpars. It implements parsimony analysis based on gene frequencies. The method was described by D. L. Swofford and S. H. Berlocher in a paper in Systematic Zoology 36: 293-325, 1987. The program is available in FORTRAN 77 source code. The search for most parsimonious trees under Swofford and Berlocher's criterion is not very extensive, Swofford notes, because the individual tree evaluations are computationally difficult. The source code in FORTRAN, with documentation, is available by anonymous ftp from onyx.si.edu in directory freqpars.

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 ftp.math.utk.edu 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) anu.edu.au) 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 http://dingo.cc.uq.edu.au/~ansblomb/. Its README file can be found in a newsgroup posting at http://life.biology.mcmaster.ca/~brian/evoldir/Other/ComparativeMethod.software.

Dopazo is now at the Centro Nacional de Investigaciones Ocológicas (jdopazo  (at) cnio.es. 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) samba.cnb.uam.es) 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 http://www.cnb.uam.es/~bioinfo/Software/Ximo/www1.html or by anonymous ftp at: ftp.cnb.uam.es in directory pub/cnb/molevol.

Dopazo is now at the Centro Nacional de Investigaciones Ocológicas (jdopazo  (at) cnio.es. 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) ggr.co.uk and carazo  (at) embnet.cnb.uam.es) 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 ftp.cnb.uam.es 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) gsk.com) 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: phylogeny.harvard.edu 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) ic.ac.uk). This program seems not to be currently available there.

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 evolve.zoo.ox.ac.uk 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) brahms.biology.rochester.edu) 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 http://brahms.biology.rochester.edu/software.html. (The C source code without the Macintosh executable is also available from the Slatkin Lab's software Web page at http://ib.berkeley.edu//labs/slatkin/software.html.)

Jongsik Chun of the School of Biological Sciences, Seoul National University, Korea (jchun  (at) snu.ac.kr) has released PHYDIT version 3.1. PHYDIT is a sequence alignment environment that can align either nucleotide or protein sequences manually or using pairwise methods, and contains some PHYLIP programs to do either neighbor-joining or least-squares phylogenies on the alignments. PHYDIT is available as a Windows executable. It is available free for noncommercial use. The user needs to register to download. The PHYDIT web page is http://plaza.snu.ac.kr/~jchun/phydit/.

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

John Huelsenbeck (johnh  (at) brahms.biology.rochester.edu) 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 http://ib.berkeley.edu//labs/slatkin/software.html.

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) sherb.lin.irk.ru) 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 http://sherb.lin.irk.ru/uo.html. 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) reading.ac.uk) 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:

• Pagel, M. 1997. Inferring evolutionary processes from phylogenies. Zoologica Scripta 26: 331-348.
• Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877-884.

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) massey.ac.nz.

 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) cs.unm.edu), Tandy Warnow (tandy  (at)  cs.utexas.edu), and Mark Miller (mmiller  (at) scsc.edu) has released version 0.2.0.0 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://www.phylo.org/sub_sections/software.htm

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

 Gráinne McGuire, currently of Taylor Fry Consulting Actuaries, Sydney, Australia (grainne  (at) taylorfry.com.au) and Frank Wright of Biomathematics and Statistics Scotland, in Dundee (frank  (at) bioss.sari.ac.uk), 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 http://www.bioss.sari.ac.uk/~frank/Genetics. A Windows interface to TOPAL, written by Iain Milne in Java, called TOPALi, is available at the TOPALi web site at http://www.bioss.ac.uk/~iainm/topali/. 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.

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 available free as C source code from the Indiana University IUBIO software archive at http://iubio.bio.indiana.edu:7780/perl/custom/index.cgi?dir=/public/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.

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)  sussex.ac.uk) and also at the Veterinary Laboratories Agency Weybridge. I do not know of any distribution of this program from any web site there.

John Maynard Smith and Noel Smith of the School of Biological Sciences of the University of Sussex (noelsmith  (at) yahoo.com) 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 http://www.biols.susx.ac.uk/Home/John_Maynard_Smith/. (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.)

The following servers have disappeared:

• This server no longer responds and that unit has no pointers to these programs on its web pages. Zharkikh is currently with Myriad Genetics in Utah. I do not know of any place distributing the programs.
  Andrey Zharkikh (zharkikh  (at) hgc6.sph.uth.tmc.edu) of the Genetics Centers at the University of Texas Health Sciences Center in Houston has programs for double-bootstrapping of nucleotide sequences, using his innovative complete-and-partial bootstrap method for getting less biased P values. They are available free by World Wide Web at http://hgc6.sph.uth.tmc.edu:8080/CP-bootstrap.dir, or by anonymous ftp at hgc6.sph.uth.tmc.edu/pub/zharkikh/double-bootstrap. His technique is described in the paper by Zharkikh, A. and W.-H. Li. 1995. Estimation of confidence in phylogeny: Complete-and-Partial bootstrap technique. Molecular Phylogenetics and Evolution 4:i 44-63 and briefly reviewed in Li, W.-H. and A. Zharkikh. 1995. Statistical tests of DNA phylogenies. Systematic Biology 44: 49-63.
• Allan Dickermann, then of the University of Arizona, had a server version of his program HyperPars which analyzed data with recombining sequences, reconstructing histories that included recombinations.
• The sUPGMA server has been discontinued as the sUPGMA program has been discontinued (see above).
  Allen Rodrigo of the Computational and Evolutionary Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand has a server which runs sUPGMA (Serial sample UPGMA). It reconstructs evolutionary histories/genealogies from distance matrices under the assumption of a molecular clock when sequences are obtained serially in time. It can also carry out UPGMA and WPGMA clustering as well as Neighbor-Joining. The Java code for sUPGMA is also available.
• Six of the servers that carried out PHYLIP analyses have now disappeared:
  • The Schering-Plough Research Institute at B oston University, Boston, Massachusetts has a server available using the Singapore software at cyrus.bu.edu/phylip/index.html.
  • The Wistar Institute at the University of Pennsylvania, in Philadelphia, has made PHYLIP available as a server using the Singapore software at http://sing.wistar.upenn.edu:8888/phylip/index.html.
  • The Internet Bioinformatics Group of the Internet Research and Development Unit of the National University of Singapore has a server at http://sdmc.krdl.org.sg:8080/~lxzhang/phylip/. (There is a different server now in Singapore -- see the list of servers).
  • Joaquin Dopazo at the Centro Nacional de Biotecnologia, Madrid, Spain has made a server available.
  • The University of Nebraska at Lincoln made available the WEBPHYLIP server originally constructed by Louxin Zhang at the National University of Singapore.
  • The Canadian Bioinformatics Resource at the NRC Institute for Marine Biosciences, Halifax, Nova Scotia made available a WEBPHYLIP server as well.
• This VOSTORG server no longer seems to exist. See the VOSTORG entry above for the status of the VOSTORG software package.
  The Section of Molecular Evolution of the Institute of Cytology and Genetics in Novosibirsk, Russia has a server at http://molevol.bionet.nsc.ru/www_vs.htm for the VOSTORG package. The server can compute distances and find UPGMA, WPGMA, or Neighbor-Joining phylogenies.
• This server seems to have gone inactive, probably long ago when the RDP project moved to Michigan State University.
  The Suggest Tree function of the old web page of the Ribosomal Database Project at the University of Illinois (the main project has now moved to Michigan State University but so far has not yet implemented this server on its web page there). You submit a large- or small-subunit ribosomal RNA sequence and this server will align it with their database of sequences, place it in the best position it can on the tree of those sequences, and return the nearby part of that tree. The server returns the results by email.
• Robertson is now at University of Manchester (david.robertson (at) manchester.ac.uk) but has not resumed the Frag_Tree/Tree server there.
  David Robertson (david  (at) igs.cnrs-mrs.fr) of the CNRS in Marseille has implemented TREE and FRAG_TREE, Neighbor-Joining servers that take a ClustalW .ALN file of aligned sequences, use ClustalW to align them and my program DRAWTREE to draw the resulting tree. TREE does the whole alignment, and FRAG_TREE a specified region of the alignment. The TREE server will be found at http://193.50.234.246/~beaudoin/anrs/Tree.html and the FRAG_TREE server will be found at http://193.50.234.246/~beaudoin/anrs/Frag.html.
• This URL suddenly went dead though Ree does have pages near there that describe his software
  Rick Ree of the Field Museum of Natural History in Chicago has a server which will draw Postscript or PDF figures of trees whose nested-parenthesis reprewsentation you provide. It uses the PHYLIP program Drawgram rather then Drawtree.
• The Cladogramer server at the Bioinformatics Center in Singapore seems to have disappeared (again). It inferred trees of haplotypes by parsimony, using the frequency of haplotypes to root the tree.

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

Japan

• a full mirror is maintained at ftp.gdbnet.ad.jp in directory ftpsync/ftp.bio.indiana.edu
• a mirror of the molbio section only is maintained at ftp.nig.ac.jp in directory pub/mirror/IUBIO/molbio

U.K.

A mirror of the molbio section is maintained at http://mic3.hensa.ac.uk/hosts/iubio.bio.indiana.edu/molbio/.

India

A mirror of the molbio section is available at imtech.chd.nic.in in directory /pub/mirror_sites/iubio/

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

• The National Biotechnology Information Facility has a list of phylogeny programs (including some population genetics programs as well) at http://www.nbif.org/links/7_1_1_12_2.php.
• The list of phylogeny software compiled by David Maddison and Wayne Maddison as part of their "Tree of Life" project on the World Wide Web. Its URL is: http://phylogeny.arizona.edu/tree/programs/programs.html. This list has not been updated in a while.
• Dan Jacobson posted an extensive list of biological software and database sites at http://www.bis.med.jhmi.edu/Dan/software/biol-links.html. It has not, as far as I know, been updated in a while.
• The European Bioinformatics Institute (EBI) has created the BioWurld index of resources, a semi-automated index of bioinformatics and molecular biology resources. It is located at http://search.ebi.ac.uk:8888/compass. The resources include Academic Institutes, Departments, and Projects, Journals and Newsletters, Commercial Sites and Services , Miscellaneous, Conferences and Courses, Online Tools and Services, Databases, Research, Educational Resources, Scientists Homepages, Employment, and Software. Users are invited to submit URLs to the index (they will decide which to include). As yet there are only a few software entries, and growth of this index has been very slow.
• The Community Software list at the CIPRes (CyberInfrastructure for Phylogenetic Research) project lists phylogeny programs produced by its members with a one-line description for each.
• The BioCatalog phylogeny page at the European Bioinformatics Institute, located at http://corba.ebi.ac.uk/Biocatalog/Phylogeny.html. Last updated in 2000. This has disappeared from the web site at EBI (www.ebi.ac.uk), but a new site called www.biocatalog.com contains a banner promising that it is being constructed. Is it the same "BioCatalog" or is it something unrelated?
• The University of California Museum of Paleontology page of Phylogenetics Software Resources at http://www.ucmp.berkeley.edu/subway/phylo/phylosoft.html. Few programs are listed, but there is a very nice list of software lists there.
• A brief list of programs at the Willi Hennig Society's home pages. It reflects a rather different worldview, centered on the parsimony method. The Hennig Society site has been reorganized and the educational material about methods eliminated, at least for now.
• Stephen A. Smith, of the Department of Ecology and Evolutionary Biology at Yale University has created the PhyCom "phylogenetic community" web site which lists news about programs, and has discussions on issues concerned with phylogenies. A login is required but this is free. This site gives every appearance of having been taken over by an exploitive operation that posts fake web sites that pretend to have real content while selling you crap.