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PHYLIP version 3.6 is my own package. It is available free, from its Web site, in C source code, or as executables for Windows, Mac OS X, and Mac OS 8 or 9. The C source code can easily be compiled on Unix or Linux systems. 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 may be the most widely-distributed phylogeny package, with about 27,000 registered users, some of them satisfied. It is fourth after PAUP*, MrBayes, and MEGA in the competition to be the program responsible for the most published trees. It has been distributed since October, 1980 and has celebrated its 27th anniversary, as the oldest distributed phylogeny package. PHYLIP is distributed at the PHYLIP web site at http://evolution.gs.washington.edu/phylip.html. A number of sites offer web-servers that will perform data analyses using PHYLIP.

David Swofford of the School of Computational Science and Information Technology, Florida State University, Tallahassee, Florida has written PAUP* (which originally meant Phylogenetic Analysis Using Parsimony). PAUP* version 4.0beta10 has been released as a provisional version by Sinauer Associates, of Sunderland, Massachusetts. It has Macintosh, PowerMac, Windows, and Unix/OpenVMS versions. PAUP* has many options and close compatibility with MacClade. It includes parsimony, distance matrix, invariants, and maximum likelihood methods and many indices and statistical tests. It is described in a web page at http://paup.csit.fsu.edu/, which also contains links to its web pages at Sinauer Associates. It is available for the following types of systems:

• For PowerMac and 68k Macintosh Mac OS 9 in a version with full mouse-windows user interface, which can also be run under the Classic environment on Mac OS X,
• For PowerPC Mac OS X systems or Intel Mac OS X systems when running under emulation) in a version with a command-line interface,
• For Windows in a version with a character-based command-line interface (which appears in a Windows window),
• For DOS or a Windows DOS box in a version which has command-line interface, and
• In a Unix/Linux version, with command-line interface, for Alpha Compaq/Digital Unix, Alpha Linux, PowerPC Linux, Intel-compatible Linux, Sun SPARC/UltraSPARC Solaris, and Alpha VMS.

MacClade is a pioneering program for interactive analysis of evolution of a variety of character types, including discrete characters and molecular sequences. It works on Macintoshes with MacOS (including MacOS X). 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. It has many other features beyond this, including ability to edit data, print out phylogenies, and even simulate the evolution of data on a tree. MacClade was written by Wayne Maddison (now of the Department of Zoology, University of British Columbia) and David Maddison of the Department of Entomology, University of Arizona. It is distributed by Sinauer Associates of Sunderland, Massachusetts USA (their company web site is http://www.sinauer.com/". For $125 they sell a CDROM with the program, help file, and example data files, plus a book (which has about 100 pages of an introduction to phylogenetic theory and 250 pages of program instructions). You can also download, after purchasing MacClade, an updater that will produce a native MacOS X executable. Site licenses are also available for a slightly less capable teachign version. MacClade is described on its Web page, at http://phylogeny.arizona.edu/macclade/macclade.html. A demonstration version of MacClade 4 is also available there.

An much earlier and less capable Version, 2.1 (which for example cannot read nucleic acid sequences and has many 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, (respectively macclade-old.hqx and 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  (at) umich.edu) and by Diana Lipscomb at George Washington University (biodl  (at) 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  (at) 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.

  Torsten Eriksson of the Bergius Botanical Garden, Stockholm, Sweden (torsten  (at) 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 5.03 is written in the scripting language Perl, and runs on most systems that have Perl installed. An earlier version for PowerMac or 68k Macintoshes is available as a Hypercard stack, and also in a standalone version that includes the Autodecay Hypercard stack plus the Hypercard runtime engine. 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/index_forskning_soft.html.

Doug Eernisse of the California State University, Fullerton (DEernisse  (at) fullerton.edu) has constructed DNA Stacks version 1.3.3, a Macintosh HyperCard stack that can carry out a variety of analyses on DNA sequences. It does not do phylogenies itself. It has an alignment editor, and can carry out various kinds of translation, and codon bias analysis. It can write out data sets in PAUP*, Hennig86, and PHYLIP formats. It is included here because in its "Support Index Blocks..." menu item it is able to prepare jobs for PAUP* to enable Decay Index (Support Index) analysis. It is available by World Wide Web from http://biology.fullerton.edu/deernisse/dnastacks.html.

Michael Sorenson of the Department of Biology, Boston University (msoren  (at) bu.edu) has released TreeRot, version 2b, a Macintosh program that helps make Bremer Support Indices ("decay indices") for parsimony analyses. It generates a PAUP* command file with a constraint statement for each node in a given shortest or strict consensus tree and with commands to search for trees inconsistent with each of these constraint statements in turn. For nodes with decay indices of more than a few steps, the constraint statement approach is much more effective than simply finding all trees 1, 2, 3, 4, etc. steps longer than the shortest tree and then examining their strict consensus for which nodes are lost. This version also supports the determination of partitioned Bremer support indices introduced in the paper: Baker, R.H., and R. DeSalle. 1997. Multiple sources of character information and the phylogeny of Hawaiian Drosophilids. Systematic Biology 46: 654-673, and it will also parse the PAUP* log file, automatically calculating the decay index for each node. A MacOS Macintosh executable and documentation is available at its web site A Macintosh executable of an earlier version is also available by anonymous ftp from ftp.vims.edu in directory other/hennig as file TreeRot.sea.bin. at http://people.bu.edu/msoren/TreeRot.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  (at) umich.edu) and Diana Lipscomb at George Washington University (BIODL  (at) 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  (at) 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  (at) 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 version of Nona which includes Piwe and SPA is available as freeware from its web page at http://www.cladistics.com/aboutNona.htm. An older version of NONA that runs on DOS is available as shareware at the ftp site ftp.vims.edu in directory other/hennig as file pars-pag.exe, a self-extracting DOS Zip file. It requires the user to hit an extra key each time they execute a command.

 Pablo Goloboff, of INSUE - Fundación e Instituto Miguel Lillo 205, 4000 S. M. de Tucumán, Argentina, (pablogolo  (at) csnat.unt.edu.ar) 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), version 1.1 of June 2007. 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. It can handle characters with discrete states as well as continuous characters. The program is distributed as Windows, Linux, and both PowerMac and Intel Mac OS X executables. The program and some support files including documentation is available from its web page at http://www.zmuc.dk/public/phylogeny/TNT It is free, provided you agree to a license with some reasonable limitations.

Derek Sikes of the University of Calgary (dsikes  (at) ucalgary.ca) and Paul Lewis of the Department of Ecology and Evolutionary Biology of the University of Connecticut have produced PAUPRat, a program that generates a text file which can be used as commands by PAUP* to have it carry implement Kevin Nixon's highly effective tree search method, the Parsimony Ratchet. The input files can be modified to implement Rutger Vos's comparable Likelihood Ratchet. It is available as Macintosh, Mac OS X and Linux executables, as a DOS executable that can be run under Windows, and in source code, from its web site at http://www.ucalgary.ca/~dsikes/software2.htm.

Frédéric Calendini and Jean-Francois Martin of the Departement Protection des plantes et environnment of the Ecole Nationale Supérieur, Montpellier, France (martinjf (at) ensam.inra.fr) have produced PaupUp version 1.0.2032.22590 Beta , a graphical frontend for Paup* DOS software . The PauUp program provides a user-friendly interface to the phylogenetic program PAUP* on the Windows operating systems. The DOS version of PAUP* is entirely command-line driven and does not provide any graphical interface. PaupUp partly resolves this issue, providing around 80% of the available commands (the most commonly used in our opinion) in a graphical environment comparable to the MAC OS version while the last 20% commands are still available through direct command-line input in a single integrated design. The programs TreeView and Modeltest can be called from PaupUp. PaupUp is not compatible with the Windows version of PAUP* but is compatible with the DOS version that is distributed with that Windows version. It is available as a Windows executable. It also requires the Microsoft .NET executable framework to be installed. PaupUp can be downloaded from its web site at http://www.agro-montpellier.fr/sppe/Recherche/JFM/PaupUp/

Kai Müller of the Nees-Institut für Biodiversit&aauml;t der Pflanzen of the University of Bonn, Germany (kaimueller (at) uni-bonn.de) has written PRAP (Parsimony Ratchet Analyses using PAUP* and likelihood) version 2.0, a Java program to drive PAUP* in comuting Bremer support of groups, and in doing ratchet searches for parsimony or likelihood trees. It allows the user to make PAUP* carry out searches using the "parsimony ratchet" strategy of Kevin Nixon. In version 2.0 this can be done using either the parsimony criterion or the likelihood criterion (in spite of the name of the search method). It can also do variations on the parsimony ratchet including multiple random addition sequences. An earlier version, 1.0, is also available here. It is described in the paper: Müller, K. F. 2004. PRAP - computation of Bremer support for large data sets. Molecular Phylogenetics and Evolution 31: 780-782, and the search strategies it implements are described in the paper: Müller, K. 2005. The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support. BMC Evolutionary Biology 5: 58. It is available as Java executables, as downloads for Windows, Mac OS X, and for Unix. It can be downloaded from its web site at http://www.nees.uni-bonn.de/downloads/PRAP2/index.htm

  MEGA (Molecular Evolutionary Genetic Analysis) is produced by Sudhir Kumar at the Department of Biology, Arizona State University, Phoeniz, Arizona (s.kumar  (at) 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 (nucleic acid sequences and protein sequences). It can do boostrapping, consensus trees, and a variety of distance measures, with Neighbor-Joining, Minimum Evolution, UPGMA, and parsimony tree methods, as a well as a variety of data editing tasks, tests of the molecular clock, and single-branch tests of significance of groups. MEGA2 is the new version, currently at version 2.1. 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. MEGA versions ara available free at its web site at http://www.megasoftware.net. MEGA2 is available free as Windows executables, with a downloadable manual. In addition, MEGA 3.0 is available as a downloadable beta release. The earlier version, MEGA is available there as a DOS executable. Its manual is also downloadable at the MEGA site and that version's manual is also available on line at http://evolgen.biol.metro-u.ac.jp/MEGA/manual/default.html.

Xuhua Xia of the Department of Biology and the Center for Advanced Research in Environmental Genomics (CAREG) of the University of Ottawa, Ontario, Canada (xxia  (at) uottawa.ca) has released DAMBE (Data Analysis in Molecular Biology and Evolution), version 4.5.53, 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, and many other features. 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 is described in two publications, a paper and a book:

• Xia, X., and Z. Xie. 2001. DAMBE: Data analysis in molecular biology and evolution. Journal of Heredity 92: 371-373, and a book:
• Xia, X. 2000. Data Analysis in Molecular Biology and Evolution. Kluwer Academic Publishers, Boston.

Alexei Drummond, Korbinian Strimmer, Ed Buckler, and Matthew Goode have released PAL (Phylogenetic Analysis Library) version 1.4, a free collection of Java classes for use in molecular phylogenetics. Their addresses are respectively:

• Alexei Drummond (alexei  (at) cs.auckland.ac.nz, Department of Computer Science, University of Auckland, New Zealand
• Korbinian Strimmer (strimmer  (at) stat.uni-muenchen.de, Department of Statistics, University of Munich
• Ed Buckler (buckler  (at) statgen.ncsu.edu), Department of Genetics, North Carolina State University
• Matthew Goode (m.goode  (at) auckland.ac.nz), School of Biological Sciences, University of Auckland, New Zealand.

• 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

• Drummond, A., and K. Strimmer. 2001. PAL: An object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17: 662-663.

• 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 Statistics of the University of Munich, Germany (korbinian.strimmer  (at) lmu.de) has released Vanilla, version 1.2, 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.

Wayne Maddison of the Departments of Zoology and Botany, University of British Columbia, Vancouver, Canada, and David Maddison of the Department of Entomology, University of Arizona, Tucson have released Mesquite, version 1.12. The project email address is info  (at) mesquiteproject.org. Mesquite is a large and varied set of modules in Java to carry out a wide variety of analyses in comparative biology. It is also intended as a framework for other developers to use to add additional functons. Some of the over 500 functions available in the project currently are:

• Reconstruction of ancestral states (parsimony, likelihood)
• Tests of process of character evolution, including correlation
• Simulation of character evolution (categorical, DNA, continuous)
• Parametric bootstrapping (with integration with programs such as PAUP* and NONA)
• Morphometrics (PCA, CVA, geometric morphometrics)
• Coalescence (simulations, other calculations)
• Tree comparisons and simulations (tree similarity, Markov speciation models)

Mesquite is available in Java source code from its web page at http://mesquiteproject.org.

Applied Maths BVBA of Keistraat 120, 9830 Sint-Martens-Latem, 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 2222 100, fax them at +32 9 2222 102, e-mail them at info  (at) applied-maths.com, or use the information request form at their web pages. Their U.S. Sales Office is at Applied Maths Inc., 512 East 11th Street, Suite 207, Austin, Texas 78701. phone +1 512-482-9700, fax +1 512-482-9708 (email is info-us (at) applied-maths.com).

John Czelusniak, then of the Department of Anatomy and Cell Biology, Wayne State University, Detroit, Michigan 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 Intel-compatible Linux systems.

Kai Müller of the Nees-Institut für Biodiversität der Pflanzen of the University of Bonn, Germany (kaimueller (at) uni-bonn.de) has produced SeqState version 1.37. It carries out a variety of primer design functions and also calculates various statistics on aligned DNA sequences. For the purposes of this listing, the relevant feature is that it can be used to implement a number of different kinds of coding of indels (insertions and deletions). It is described in the paper: Müller K. F. 2005. SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics 4: 65-69 and the different indel coding methods are discussed in two other papers:

• Müller, K. F. 2006. Incorporating information from length-mutational events into phylogenetic analysis. Molecular Phylogenetics and Evolution 38: 667-676.
• Simmons, M. P., K. F. Müller, A. P. Norton. 2007. The relative performance of indel-coding methods in simulations. Molecular Phylogenetics and Evolution 44: 724-740.

Naoko Takezaki of the Center for Information Biology, National Institute of Genetics, Mishima, Japan, (ntakezak  (at) lab.nig.ac.jp) 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 is distributed as C source code for Unix by ftp from its ftp site at ftp://ftp.nig.ac.jp/pub/Bio/gmaes/, and also by ftp from the IUBIO archive at http://iubio.bio.indiana.edu/soft/molbio/evolve/.

Chris Creevey and James McInerney of the Bioinformatics and Pharmacogenomics Laboratory of the National University of Ireland, Maynooth (chris.creevey (at) may.ie) have released CRANN (an Irish word for "tree"), version 1.04, a program to detect natural selection using rates of synonymous and nonsynonymous substitutions. Crann takes FASTA format aligned nucleotide sequence files and either infers a tree using neighbor-joining based on nonsynonymous differences, or allows the user to read in a tree. It reconstructs the placements of the synonymous and nonsynonymous substitutions on the tree, and carries out a statistical test for an excess of nonsynonymous changes. It can also calculate synonymous and nonsynonymous differences between all pairs of sequences, and can also do that in a sliding window along the sequences. It is described in the papers:

• Creevey, C. and J. O. McInerney. 2003. CRANN: Detecting adaptive evolution in protein-coding DNA sequences. Bioinformatics 19: 1726.
• Creevey, C. and J. O. McInerney. 2002. An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene 300: 43-51.

Mathieu Blanchette, of the School of Computer Science, McGill University, Montréal, Québec (blanchem  (at) mcb.mcgill.edu) and Martin Tompa of the Department of Computer Science and Engineering at the University of Washington, Seattle (tompa  (at) cs.washington.edu) have released FootPrinter2.1, a program that uses parsimony scores to carry out "phylogenetic footprinting" to search for regulatory sequences in the vicinity of genes that have been sequenced in multiple species. The program looks for locations upstream of each gene which, when taken together on a known phylogeny, show the largest amount of conservation by having the smallest number of changes of state along the tree. The method is described in these papers:

• Blanchette, M. and M. Tompa. 2003. FootPrinter: a program designed for phylogenetic footprinting. Nucleic Acids Research 31: 3840-3842.
• Blanchette, M. and M. Tompa. 2002. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 12: 739-748.
• Blanchette, M., B. Schwikowski, and M. Tompa. Algorithms for phylogenetic footprinting. Journal of Computational Biology 9: 211-223.

  Daniel Barker (db60 (at) st-andrews.ac.uk) of the University of St. Andrews, Scotland, U.K., has written LVB version 2.1, 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 with ambiguous nucleotides and/or discrete morphological characters can be used. Bootstrapping of the data is also supported. The program is currently available in ANSI C source code as a Unix tar file, and as executables for Windows, MacOS X, and Linux. The text of a manual can also be read or downloaded from the web site. LVB is available from its Web site at http://biology.st-andrews.ac.uk/cegg/lvb.htm. It is also available as a Web server from the Institut Pasteur.

Dick Hwang of the Department of Genome Sciences, University of Washington (dhwang  (at) u.washington.edu) has written GAPars, a program using a genetic algorithm to search for most parsimonious phylogenies. The program is written in C++ and should compile on Unix C++ compilers and on most other C++ compilers. He describes it as working "rather inefficiently" and "not ready for prime-time use". It can be obtained by emailing Hwang at the address above.

Quinn Snell, Mark Clement and Hyrum Carroll of the Computational Science Laboratory of the Department of Computer Science at Brigham Young University. Povo, Utah (clement (at) cs.byu.edu) have written PSODA, a parsimony program for nucleotide sequences. The program reads the NEXUS file format, and carries out heuristic rearrangement of trees using the parsimony criterion. It is available as C++ source code, Windows executables, Linux executables and Powermac Mac OS X executables. It can be downloaded from its web site at http://dna.cs.byu.edu/psoda/

Rod Page (r.page  (at) bio.gla.ac.uk), of the Division of Environmental and Evolutionary Biology of the University of Glasgow has released GeneTree, version 1.3.0, 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 Macintosh executable and as an executable for Windows. 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  (at) biomail.ucsd.edu) of the Section of Ecology, Behavior and Evolution, University of California, San Diego 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 C source code that can be compiled for Unix from Jonathan Bollback's software web page at http://www.binf.ku.dk/~bollback/software.html. A Macintosh version that was formerly distributed seems not be available any more.

Mark Clement, David Posada, and Keith Crandall of the Universidad Vigo, Spain (Posada) and the Department of Zoology, Brigham Young University, Provo, Utah (dposada  (at) uvigo.es) have released TCS version 1.21, 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://darwin.uvigo.es/software/tcs.html.

David Posada (dposada  (at) uvigo.es), of the Universidad Vigo, Spain, Keith Crandall, of the Department of Zoology, Brigham Young University, Provo, Utah (Keith_Crandall  (at) byu.edu) and Alan Templeton, of the Department of Biology of Washington University, Saint Louis, Missouri (temple_a  (at) biology.wustl.edu) have made available GEODIS (version 2.4). It implements Templeton's method of Nested Clade Analysis, which is intended to distinguish between historical divergence of populations and geographical separation, using the geographical distribution of haplotypes in a genealogy. GEODIS is a Java program which can run on any platform. It is described in a paper: Posada D., K. A. Crandall and A. R. Templeton. 2000. GeoDis: A program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9: 487-488. It is available at its web site at http://darwin.uvigo.es/geodis.html

Jon Jeffery (jon (at) donnasaxby.com), then of the Insitute of Biology, Leiden University, The Netherlands has written Parsimov, a series of Perl scripts to implement "event cracking", a parsimony-based method of finding the minimum number of changes in developmental sequences of events that are necessary to explain the evolution of pairs of characters on a tree. Among the uses of this method is to reconstruct ancestral developmental sequences. The programs include:

• Parsimv7g.pl which implements event-pair "parsimony cracking".
• ReplacerParsimv.pl which takes a Parsimv7g.pl output file and replaces the PAUP* character numbers with more readable character names according to a user-specified text list.
• Describe.pl, which creates a PAUP* command file to describe each tree in memory under ACCTRAN and DELTRAN optimizations (saving each as separate log files) plus a Parsimv7g.pl batch file (e.g., ParsBatch.txt) to crack each of the PAUP* log files produced.

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