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PHYLIP version 3.5c is my own package. It is available free, from its Web site, in C source code, or as executables for pre-386 DOS, 386/486/Pentium DOS, Windows 3.1, Windows95/98/NT, 68k Macintosh, or PowerMac. The C source code is easily compiled on Unix systems, and VMS compilation support is also available in the package. It includes programs to carry out parsimony, distance matrix methods, maximum likelihood, and other methods on a variety of types of data, including DNA and RNA sequences, protein sequences, restriction sites, 0/1 discrete characters data, gene frequencies, continuous characters and distance matrices. It is the most widely-distributed phylogeny package, with over 7,000 registered users, some of them satisfied. It competes with PAUP* to be the program responsible for the most published trees. It has been distributed since October, 1980. PHYLIP is distributed at the PHYLIP web site at http://evolution.genetics.washington.edu, or by anonymous ftp from evolution.genetics.washington.edu in directory pub/phylip.

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David Swofford of the Laboratory of Molecular Systematics, National Museum of Natural History, Smithsonian Instition, Washington, D.C. has written PAUP* (which originally meant Phylogenetic Analysis Using Parsimony). PAUP* version 4.0beta has been released as a provisional version by Sinauer Associates, of Sunderland, Massachusetts. It has Macintosh, PowerMac, Windows, and Unix/OpenVMS versions. PAUP* is the most sophisticated parsimony program, with many options and close compatibility with MacClade. It has become much broader with the inclusion of more methods. It includes parsimony, distance matrix, invariants, and maximum likelihood methods and many indices and statistical tests. Version It is described in a web page at http://www.sinauer.com/Titles/frswofford.htm, and in more detail at its web site at the LMS at http://www.lms.si.edu/PAUP/about.html. It is available for the following types of systems:

• For PowerMacs and 68k Macintoshes in a version with full mouse-windows user interface,
• For Windows95, Windows98, or WindowsNT in a version with a character-based command-line interface (which appears in a Windows window),
• For DOS or a Windows (3.1, 95, 98 or NT) DOS box in a version which has command-line interface, and
• In a Unix/VMS version, with command-line interface, for Alpha Compaq/Digital Unix, Alpha Linux, PowerPC Linux, Intel-compatible Linux, Sun SPARC/UltraSPARC Solaris, and Alpha VMS1.

If you have a Macintosh computer and any interest in discrete-state parsimony methods (including DNA and protein parsimony), you should definitely get MacClade. It was written by Wayne Maddison and David Maddison of the University of Arizona. All distribution is by Sinauer Associates, 23 Plumtree Road, Sunderland, Massachusetts 01375-0407, USA. The Sinauer Associates web page for MacClade is at http://www.webcom.com/~sinauer/system.shtml#Maddison. Sinauer's phone number is: (413) 549-4300 and their fax number is (413) 549 1118. A disk with program, help file, and example data files, plus book (which has about 100 pages of intro to phylogenetic theory, and 250 pages of program instructions), is $100 U.S. ($40 for the book alone). Site licenses are also available. MacClade is described on its Web page, at http://phylogeny.arizona.edu/macclade/macclade.html. A demonstration version of MacClade 3 is also available there. MacClade enables you to use the mouse-window interface to specify and rearrange phylogenies by hand, and watch the number of character steps and the distribution of states of a given character on the tree change as you do so.

An earlier and less capable Version, 2.1 (which for example cannot read nucleic acid sequences and has fewer features for discrete characters) is also available by anonymous ftp from the EMBL and Indiana molecular biology software servers at (respectively) ftp.bio.indiana.edu, and ftp.ebi.ac.uk, in directories molbio/mac and pub/software/mac, respectively, as a BinHexed and squeezed archive, macclade21.hqx.

J. S. Farris has produced Hennig86, a fast parsimony program including branch-and-bound search for most parsimonious trees and interactive tree rearrangement. Although complete benchmarks have not been published it is said to be faster than Swofford's PAUP*; both are a great many times faster than the parsimony programs in PHYLIP. The program is distributed in executable object code only and costs $50, plus $5 mailing costs ($10 outside of of the U.S.). The user's name should be stated, as copies are personalized as a copy- protection measure. It is distributed by Arnold Kluge, Amphibians and Reptiles, Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079, U.S.A. (akluge@umich.edu) and by Diana Lipscomb at George Washington University (biodl@gwuvm.gwu.edu). It runs on PC-compatible microcomputers with at least 512K of RAM and needs no math coprocessor or graphics monitor. It can handle up to 180 taxa and 999 characters. It was described in the paper: Farris, J.S. 1989, Hennig86: a PC-DOS program for phylogenetic analysis. Cladistics 5: 163.

Mark Siddall, Assistant Curator of Annelida at the American Museum of Natural History, New York (siddall@amnh.org) has released Random Cladistics, version 4.0.3, a set of programs that can carry out bootstrapping, jackknifing, a variety of kinds of permutation tests, and search for "islands" of trees, using Hennig86 or NONA to analyze the data. It can also mark ranges of sites for inclusion or exclusion, compare trees from the analyses, compute an index of incongruence between data sets, and do many other operations. To use it you must have a copy of Hennig86 (for whose distribution see above). Random Cladistics will carry out the appropriate transformations of your data and will call Hennig86 and have it analyze them, and then it will summarize the results. Random Cladistics is described by its author as no longer being supported software -- he says that "Winclada is far superior and provide's a nice interface." Random Cladistics is distributed by its author from its web site at http://research.amnh.org/~siddall/rc.html as DOS executables.

Tiago Ramos of the Museu de Zoologia, Universidade de Sao Paulo, Sao Paulo, Brazil (tcramos@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.

Torsten Eriksson of the Bergius Foundation of the Swedish Aacademy of Sciences, Stockholm, (torsten@bergianska.se) has written a program, AutoDecay which generates Decay Indices from an existing PAUP* 4.0 treefile. It is intended to simplify the the task of creating reverse constraint trees in PAUP* 4.0 and subsequent generation of Bremer support values. (Bremer, K. 1994. Cladistics 10: 295-304). AutoDecay version 3.0 is available for PowerMac or 68k Macintoshes, in standalone versions that include the Autodecay Hypercard stack plus the Hypercard runtime engine. It is also available as a smaller Hypercard stack which requires that you have Hypercard or Hypercard Player. An older C program compiled for the Macintosh also is available, which may not work with recent versions of PAUP*. Autodecay can be obtained by World Wide Web from http://www.bergianska.se/personal/TorstenE/.

James Lyons-Weiler of the Biological Sciences Department of the University of Massachusetts, Lowell (James_LyonsWeiler@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.

J. S. Farris has recently released RA (Rapid nucleotide Analysis). It features rapid bootstrapping. It is available from Arnold Kluge, Amphibians and Reptiles, Museum of Zoology, University of Michigan, Ann Arbor, Michigan 48109-1079, U.S.A. (akluge@umich.edu) and Diana Lipscomb at George Washington University (BIODL@gwuvm.gwu.edu) who may be contacted for details. The cost is said to be about $30 US.

Kevin Nixon of the L. H. Bailey Hortorium at Cornell University in Ithaca, New York (kcn2@cornell.edu) has written WINCLADA version 0.9.99m24, an interactive program that can read and edit trees and data files, display character state changes inferred by parsimony on diagrams of the trees, and launch runs of the programs NONA, PIWE, and Hennig86. WINCLADA is available as a Windows95/98/NT executable from its web site at http://www.cladistics.com/about_winc.htm. It is available on a shareware basis: the user who downloads it must pay $50 to Kevin Nixon at Winclada/Kevin C. Nixon, 2210 Ellis Hollow Road, Ithaca, New York 14850. There is also a $200-per-class fee for its use in courses. WINCLADA supersedes and combines features of Nixon's earlier programs ClaDOS and DADA, which are no longer distributed.

Pablo Goloboff, of INSUE - Fundación e Instituto Miguel Lillo 205, 4000 S. M. de Tucumán, Argentina ((instlillo@infovia.com.ar with Subject line "para Pablo Goloboff") has written Nona (Noname), version 2.0, PiWe (Parsimony with Implied WEights), and SPA to carry out parsimony including weighted parsimony analyses. Nona searches for most parsimonious trees according to character weights defined by the user a priori. Pee-Wee calculates weights of the characters by a method introduced by Goloboff, a noniterative version of J. S. Farris's "successive weighting". It was described in Goloboff's paper in Cladistics 9: 83-91, 1993. SPA is a generalized parsimony program that allows differential weighting of changes between different states. Nona is said to be faster than other parsimony programs. A Windows 95/98/NT version of Nona which includes the functionality of Piwe and SPA is available as shareware (with a free 30-day trial period) from its web page at http://www.cladistics.com/about_nona.htm. The shareware fee of $40 should be paid to the author at the above address or to James M. Carpenter, Department of Entomology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024. Send the money and the name in which the copies are to be registered. Older versions of these programs are available as shareware at two ftp sites:

• A version (an older Window one?) of the NONA, Pee-Wee, SPA, PHAST and X-Piwe programs can be found at ftp.aki.ku.dk in directory ZMUC/golo/.
• An earlier demo version of these programs which runs on DOS. It requires the user to hit an extra key each time they execute a command. It can be found at ftp.vims.edu in directory other/hennig as file pars-pag.exe, a self-extracting DOS Zip file.

Pablo Goloboff, of INSUE - Fundación e Instituto Miguel Lillo 205, 4000 S. M. de Tucumán, Argentina, (instlillo@infovia.com.ar with Subject line "para Pablo Goloboff") together with J. S. Farris of the, Laboratory of Molecular Systematics of the Naturhistoriska Riksmuseet, Stockholm, Sweden and Kevin Nixon of the L. H. Bailey Hortorium, Cornell University, Ithaca, New York, have produced TNT (Tree analysis using New Technology), currently in a beta version. This is a parsimony program intended for use on very large data sets. It makes use of the methods for speeding up parsimony searches introduced by Goloboff in the paper: Goloboff, P.A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15: 415-428, and the highly effective "parsimony ratchet" search strategy introduced by Nixon in the paper: Nixon, K.C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15: 407-414. TNT is a The program is distributed as a Windows executable (actually I am not sure whether TNT is a Windows or a DOS program -- I assume the former). It is available from its web page at http://www.cladistics.com/webtnt.html. The program cannot be run without a password, which the user must request from Goloboff by e-mail. The user should explain why it will assist them in their analysis -- they are not interested in distributing it "just for the curious".

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@massey.ac.nz.

MEGA (Molecular Evolutionary Genetic Analysis) is produced by Sudhir Kumar at the Department of Biology, Arizona State University, Phoeniz, Arizona (s.kumar@asu.edu) together with Koichiro Tamura of Tokyo Metropolitan University and Masatoshi Nei, and Ingrid Jakobsen of Pennsylvania State University. It carries out parsimony, distance matrix and likelihood methods for molecular data. MEGA2 is the new version, currently at build 3.0 of the beta version. The previous version, MEGA, was a DOS program which carried out parsimony as well as neighbor-joining methods, with branch-and-bound search available for parsimony and bootstrapping available for all methods. MEGA2 is available as Windows95/98/NT/2000 executables and MEGA is available as a DOS executable, both from its web site at http://www.megasoftware.net. The MEGA manual is also available on-line in HTML at http://evolgen.biol.metro-u.ac.jp/MEGA/manual/default.html.

Xuhua Xia of the Department of Ecology and Biodiversity of the University of Hong Kong (xxia@hkusua.hku.hk) has released DAMBE (Data Analysis in Molecular Biology and Evolution), version 4.0.24, a general-purpose package for DNA and protein sequence phylogenies, and also gene frequencies. It can read and convert a number of file formats, and has many features for descriptive statistics. It can compute a number of commonly-used distance matrix measures and infer phylogenies by parsimony, distance, or likelihood methods, including bootstrapping (by sites or by codons) and jackknifing. There are a number of kinds of statistical tests of trees available. It can also display phylogenies. DAMBE includes a copy of ClustalW; there is also code from PHYLIP. An interesting feature is a simple web browser that allows sequences to be fetched over the web while running DAMBE. DAMBE consists of Windows95/98/NT executables. It is available from its web site at http://web.hku.hk/~xxia/software/software.htm.

Alexei Drummond and Korbinian Strimmer, respectively of the School of Biological Sciences, University of Auckland, Auckland, New Zealand (a.drummond@auckland.ac.nz), and the Department of Zoology, University of Oxford, Oxford, U.K. (korbinian.strimmer@zoo.ox.ac.uk), have released PAL (Phylogenetic Analysis Library) version 1.1, a free collection of Java classes for use in molecular phylogenetics. It is intended to facilitate the rapid construction of both general applications as well as special-purpose tools for phylogenetic analysis. PAL focuses on probabilistic data modelling and provides, e.g., routines for

• maximum likelihood, neighbor-joining and least squares analysis
• probability models for nucleotide/amino acid substitution, including constraints for a molecular clock
• bootstrapping, and the Kishino-Hasegawa-Templeton and Shimodaira-Hasegawa tests
• simulation of trees and data sets, including coalescent trees with growing populations and serial samples
• reading and write trees and alignments
• adjusting for rate variation among sites

• Vanilla (by Strimmer): A simple text front end
• Pebble (vCEBL) (by Drummond): A GUI interface to PAL plus a functional command language.

Korbinian Strimmer, of the Department of Zoology, University of Oxford, Oxford, U.K. (korbinian.strimmer@zoo.ox.ac.uk) has released Vanilla, a character-based interface to the PAL Java classes, which includes a number of programs carrying out different kinds of phylogenetic analysis:

• MLDIST which computes maximum likelihood distances between DNA sequences, protein sequences, and two-state data, with correction for unequal rates at different sites. It has many different substitution models available.
• MLTREE which computes the likelihood of a given tree under the same models as MLDIST, allowing branch lengths to be provided or to be estimated by the program, with the possibility of constraining them to be clocklike.
• EVOLVE simulates data along a tree using the above models.
• DISTTREE computes least squares branch lengths from distance matrices on a given tree, and can also construct Neighbor-Joining and UPGMA trees.

Applied Maths BVBA of Risquons-Toutstraat 38, 8511 Kortrijk, Belgium has released Bionumerics, a program to manage a wide variety of biological data "from phenotypical tests and arrays to protein and nucleic acid sequences, and including all kinds of fingerprints." In addition to database and image processing capabilities, it can do clustering and phylogenetic inference. A variety of clustering methods including UPGMA and neighbor-joining distance matrix methods are available, and for inferring phylogenies generalized parsimony and maximum likelihood are available. There are also facilities for plotting the trees. ionumerics is distributed as Windows executables. Bionumerics is commercial software. Information about it is available at its web site at http://www.applied-maths.com/bn/bn.htm. For price and ordering information contact them by phone at +32 9 22222 100, fax them at +32 9 2222 102, e-mail them at info@applied-maths.com, or use the information request form at their web pages. Their U.S. Sales Office is at Applied Maths Inc., 7301 Burnet Road, Suite 102 #226, Austin, Texas 78757, phone +1 512 454 4240, fax +1 512 300 9139. (One company vending Bionumerics sells the whole package for $26,920, though if only the sequence data module and the cluster analysis module are ordered the price is $7,170).

John Czelusniak of the Department of Anatomy and Cell Biology, Wayne State University, Detroit, Michigan (jc@tree.roc.wayne.edu) has written sog, a C program demonstrating an algorithm to find the most parsimonious phylogeny along with the parsimony strength of grouping (or Bremer decay index) for nucleotide sequences in one pass of a branch and bound algorithm. This differs from the implementation in PAUP* which uses a separate branch and bound search to find the strength of grouping for each group in the tree, using the tree group exclusion option. John says that "sog is a rather ugly hack which will be optimized and streamlined. It IS ALPHA SOFTWARE, which means it has not been tested extensively on datasets other than our primate datasets." It is available by anonymous ftp from ftp.bio.indiana.edu in directory molbio/evolve. It is distributed as C source code. It will compile and run on Linux and Nextstep for Intel systems.

Naoko Takezaki (ntakezak@lab.nig.ac.jp) of the Center for Information Biology, National Institute of Genetics, Mishima, Japan, has written gmaes, a program that estimates a gamma distribution parameter for rate variation among sites by counting the minimum number of substitutions at each site for a given tree topology. The program runs on the Sun workstations. It is distributed as C source code for Unix along with a neighbor-joining program njboot from her web site at http://cib.nig.ac.jp/dda/ntakezak.html#gmaes, and by ftp from the IUBIO archive (ftp.bio.indiana.edu) in directory molbio/evolve.

Daniel Barker (d.barker@reading.ac.uk) of the University of Reading, UK, has written LVB version 1.0, a program for inferring phylogenies using parsimony and simulated annealing. Simulated annealing is intended to allow searches for most parsimonious trees with large numbers of species. It is described as often giving good results with large matrices. Up to 16383 objects and 32766 characters may be used. Aligned nucleotide sequences and/or discrete morphological characters can be used. The program is currently available in ANSI C source code as a Unix tar file, and as executables for PowerMac, for Windows95, for Windows 3.1, and for OS/2. The text of a manual can also be downloaded from the web site. LVB is available from its Web site at http://www.rubic.reading.ac.uk/lvb. It is also available as a Web server from the Institut Pasteur.

Rod Page (r.page@bio.gla.ac.uk), of the Division of Environmental and Evolutionary Biology of the University of Glasgow has released GeneTree, a program that produces "reconciled trees" that fit a tree of gene copies to a species tree. It uses a parsimony criterion where the penalty is the number of deletions and duplications required to reconcile the gene tree with the species tree. The program is described as "preliminary". The algorithm is described in the paper: Page, R. D. M. and M. A. Charleston. 1997. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Molecular Phylogenetics and Evolution 7: 231-240. It is available as a PowerMac executable and as an executable for Windows 95 or Windows NT. They are available from the GeneTree web site at http://taxonomy.zoology.gla.ac.uk/rod/genetree/genetree.html. A manual is also available online there.

John Huelsenbeck (johnh@brahms.biology.rochester.edu) of the Department of Biology of the University of Rochester, in Rochester. New York has released CodonBootstrap version 1.0. This is a utility that will generate non-parametric bootstrap data sets from a DNA sequence file. The program re-samples codons to (1) avoid problems when analysing data under models that assume coding structure (e.g., rates partitioned by sites), or (2) when the user wishes to re-sample sites and maintain the original autocorrelation among positions within the codon. CodonBootstrap is available as a PowerMac executable from the Huelsenbeck laboratory software web site at http://johnh@brahms.biology.rochester.edu/software.html.

Ben Salisbury (ben@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@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/.

Mark Clement and David Posada of the Department of Zoology, Brigham Young University, Provo, Utah (dp47@email.byu.edu) have released TCS version 1.06, a program for estimating gene genealogies within a population. It does so by using the method introduced in the paper: Templeton, A. R., K. A. Crandall and C. F. Sing. 1992. A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132: 619-633. This is a method that connects existing haplotypes in a minimum spanning tree which is essentially a parsimony method. It can also infer networks with loops in them. TCS is written in Java and has a graphic user interface for the display of the resulting networks. It may be run on any system that has the Java runtime environment. The program is described in the paper: Clement M., D. Posada, and K. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1660. It implements the estimation of the 95% parsimony connection limit, and the estimation of outgroup weights (which are used to designate the root of the tree). It takes as input sequence files in NEXUS or PHYLIP format, and accepts absolute distances between sequences as input. The output is a Postscript picture of the tree, which can be saved as a Postscript file. TCS is available as Java executables, with documentation, at its web site at http://bioag.byu.edu/zoology/crandall_lab/tcs.htm.

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