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Phylogenetic Analysis Computer Programs
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Phylogenetic Analysis Computer Programs

Here is a list of some programs we know of that perform some sort of phylogenetic analysis, or which we think might be useful to phylogeneticists. This list is far from complete, and more programs will be added, as well as more information about the listed programs.

Many of the following descriptions were provided by the authors of the programs.

If you wish to contribute a description of your program, please send an e-mail note to tree@ag.arizona.edu.

Two other lists of phylogenetics software include Joe Felsenstein's Phylogeny Programs Available Elsewhere and the Willi Hennig Society's Page on Parsimony Analysis Software, maintained by Mark Siddall.

tree inference
CAFCA (a Collection of APL Functions for Cladistic Analysis)
FreqPars
Hennig86
An MS-DOS program for inferring phylogenies using parsimony.
MEGA (Molecular Evolutionary Genetics Analysis)
Phylogeny inference using various distance methods (including UPGMA and Neighbor-Joining with variety of distance measures) and parsimony. Various other statistics for sequence data. For DNA, RNA and protein sequence data.
PAUP
A Macintosh program for inferring phylogenies using parsimony, with many features for tree searches, tree output, and so on.
Phylip
PHYLIP is a package of 31 programs for inferring phylogenies.
PUZZLE
Random Cladistics
RNA (Rapid Nucleotide Analysis)
Spectrum
TREECON
VOSTORG
A package of microcomputer programs for sequence analysis and construction of phylogenetic trees.
WTDPARS
alignment
Clustal V
DCSE
TreeAlign
character evolution
CAIC (Comparative Analysis of Independent Contrasts)
CLADOS
COMPARE
MacClade
A Macintosh program for graphically manipulating phylogenies and studying character evolution upon them.
tree studies
COMPONENT
STATGEOM
TreeMap
Treeview

CAFCA (a Collection of APL Functions for Cladistic Analysis)

by Rino Zandee

Version: 1.5e

Computer Requirements: CAFCA is available for Apple Macintosh (system 6 or later) and PowerMac computers. Although APL is an interpreted language, the program is distributed as a stand-alone executable.

Description: CAFCA is a Macintosh program for inferring cladogenetic trees. It implements the group- and component compatibility method. In this method cladograms are seen as cliques of sets of terminal and internal nodes (components). In contrast to standard parsimony methods CAFCA does not find cladograms by exploring a search space looking for cladograms that maximize an optimality criterion expressing a property of a cladogram in terms of the characters available, like cladogram length. Instead, CAFCA explores a search space looking for cladograms with maximum resolution given the components available. Components can be characterized in terms of character states in various ways. They can be defined either as monothetic sets, or based on all possible (semi-)additive binary codings for each character, or through three-taxon-statement-permutations. The collection of cladograms found in this way can be delimited further by applying different optimimality criteria (CI and RI, AUCC, corrected extra length, compatible character state index). The program comes with example data files. Documentation is available separately from the CAFCA's WWW site as several files in PDF format (requires Acrobat Reader).

Obtaining the software: CAFCA and its documentation is distributed free and is available from CAFCA's WWW site.

Internet information: Check out CAFCA's WWW site.

FreqPars

by David L. Swofford

Hennig86

by J.S. Farris

Version: 1.5

MEGA (Molecular Evolutionary Genetics Analysis)

by Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei

Version: 1.01

Computer Requirements: Runs on all IBM and IBM-compatible PC's. Requires a hard disk, 640KB RAM memory and DOS 3.3 or later or can run on OS/2 and Microsoft Windows using DOS. Does not require extended and expanded memories, graphics adapters or math co- processors.

Obtaining the software: Contact Joyce White or the authors at: Institute of Molecular Evolutionary Genetics, 328 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802. Diskette and user manual is sent for "a nominal fee", currently $15.00. imeg@psuvm.psu.edu Fax: (814) 863-7336

PAUP

by David L. Swofford

Version: 3.1.1

Computer Requirements: Version 3 only runs on Apple Macintosh computers; version 4 will be available for Macintosh (including a PowerMac version), UNIX, and MSDOS.

Description: Version 3 is a program for inferring phylogenies using parsimony analysis (as well as Lake's invariants). (Version 4 will include maximum likelihood and distance methods.)

Obtaining the software: Currently, version 3.1.1 of PAUP is not available. Version 4 is likely to be available from Sinauer Associates in September of 1996. The program (for Power PC native, DOS/Windows, Macintosh and PowerMac, UNIX-DEC Alpha workstation and UNIX-Sun Spark workstation) and user's book is tentatively priced at $100.00. Contact scavotto@sinauer.com for more information.

Internet information: ftp site: ftp://onyx.si.edu/paup

Phylip

by Joe Felsenstein

Computer Requirements: Programs are available for 386 DOS, 386 Windows, pre-386 DOS, Macintosh, and PowerMac. The C source code can be compiled on most anything else.

Description: PHYLIP includes programs to do parsimony, distance matrix, and maximum likelihood methods for a variety of data types, including molecular sequences (DNA and protein), gene frequencies, continuous characters, discrete (0,1) characters, and restriction sites. It also includes programs to plot phylogenies and to do consensus trees. PHYLIP is the most widely distributed phylogeny package, with over 2,500 registered users, some of them satisfied. (Joe wrote that, not us!)

Obtaining the software: It is distributed free and is available from Phylip's WWW site. It is distributed in source code in C and Pascal, with extensive documentation files. Executables are also available by ftp for 386 DOS, 386 Windows, pre-386 DOS, Macintosh, and PowerMac. The C source code also compiles easily on most workstations. The source code distribution includes the documentation for all the programs.

Internet information: Check out Phylip's WWW site.

PUZZLE

by Korbinian Strimmer Arndt von Haeseler

Computer Requirements: MacOS, MS-DOS, UNIX, VMS

Description: PUZZLE is an ANSI C compliant and PHYLIP compatible program that implements the quartet puzzling method for reconstructing tree topologies from character state data. Quartet puzzling is a method that applies maximum likelihood tree recon- struction to all possible quartets of taxa and subsequently tries to combine most of the four-taxa maximum likelihood trees to construct an overall tree. Usually there are several possible solutions. A consensus tree generated from the quartet puzzling trees shows nodes that are well supported. More details about the algorithm and on the phylogenetic accuracy will be published elsewhere (K. Strimmer and A. von Haeseler, 1996). PUZZLE supports all popular models of sequence evolution of nucleotides and proteins. PUZZLE is platform independent and runs sucessfully on a large variety of computers under many operation systems, including MacOS, MS-DOS, UNIX, and VMS. Precompiled executables are provided for MacOS and MS-DOS. For UNIX and VMS system specific files for automated compilation are provided.

Obtaining the software: The following versions of PUZZLE can be obtained via ftp from the European Bioinformatics Institute (Hinxton Hall, Hinxton, Cambridge CB10 1RQ, UK): On request the PUZZLE package will also be emailed (MIME) to users who can't access these Internet servers. Users without access to the Internet should contact the authors for an alternative way of distribution.

Internet information: More information can be found at the following ftp site: ftp://fx.zi.biologie.uni-muenchen.de/pub/puzzle.

Random Cladistics

by Mark E. Siddall

Version: 2.1.1

Computer Requirements: Random Cladistics requires 1) an IBM PC or compatible running any version of MS-DOS, 2) that you have Hennig86 [SS.COM] on PATH or in the working directory. Random Cladistics will happily run as a DOS-app through Windows.

Description: Random Cladistics is a package of executables which will perform a variety of randomization-based manipulations in relation to phylogenetic data. These manipulations include conventional and unconventional BOOTSTRAPPING, the JACKKNIFE monophyly index, the Permutation-Tail-Probability test, random tree histograms and SKEWNESS, and Phylogenetic-Covariance-Probability test for confidence values in biogeographic or host-parasite coevolutionary questions. Random Cladistics runs as a shell around Hennig86 (copyright J. S. Farris) by preparing appropriate input for auto-invoked batch execution through ss.com, followed by interpretation of the results. Random Cladistics requires the user to be Hennig86-literate. Included in the package are printable "Hennig86 Simplified" and "Random Cladistics" manuals as well as on-line help with both.

Obtaining the software: Random Cladistics can be obtained at no cost by anonymous ftp to zoo.toronto.edu/pub as a self-extracting utility random.exe. Or by sending a formatted diskette to Mark E. Siddall, Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA.

Internet information: Get random.exe from zoo.toronto.edu/pub.

RNA (Rapid Nucleotide Analysis)

by J. S. Farris

Spectrum

by Michael Charleston

Version: 1.0

Computer Requirements: Spectrum requires either a Macintosh or Power Macintosh running System 7.0 or later.

Description: Spectrum is a Macintosh program to read in phylogenetic 4-state or binary data in NEXUS format, and output the bipartition spectra corresponding to the data. You can also use it to find the tree whose expected spectrum is closest to your observed spectrum. Spectrum outputs spectra in Excel format as tab-delimited text files and trees as NEXUS files which can be viewed by TreeView.

Obtaining the software: Spectrum can be obtained from the Spectru m WWW site.

Internet information: Spectru m WWW site.

TREECON

by Yves Van de Peer

Version: 3.0

Computer Requirements: MSDOS, Windows; 386 or higher, VGA card

Description: see CABIOS 9:177-182

Internet information: See the TREECON WWW site.

VOSTORG

by A. Zharkikh, A. Rzhetsky, P. Morosov, T. Sitnikova, and J. Krushkal.

Computer Requirements: MS DOS 286 or higher, about 1 Mb of hard disk space.

Description: VOSTORG is a package of programs for phylogenetic analysis of nucleotide or amino acid sequences. It includes programs for sequence input/editing, pairwise alignment, dot matrix plot, alignment editing. Tree construction is based on distance matrices or maximum parsimony principle. Tree viewer/editor allows interactive modification of tree topology. See Gene, 101 (1991) 251-254.

Obtaining the software: It is distributed free and is available from VOSTORG WWW Page

WTDPARS

by Walter Fitch

Clustal V

by Des Higgins

DCSE

by Peter De Rijk

Description: An alignment program

Internet information: See the DCSE WWW site.

TreeAlign

by Jotun Hein

CAIC (Comparative Analysis of Independent Contrasts)

by Andy Purvis and Andrew Rambaut

Version: 2.0

Computer Requirements: This version runs on any Macintosh having System 6 or later, and requires less than 500kb of RAM.

Description: CAIC (Comparative Analysis by Independent Contrasts) is a computer package for the Apple Macintosh that implements a suite of 'phylogenetically correct' comparative methods for data sets including continuous variables. Because closely-related species tend to be similar because of shared inheritance, rather than through independent adaptation, ordinary statistics such as correlation and regression cannot validly be used with comparative data. CAIC overcomes the problem of non-independence by using Felsenstein's (1985; Am. Nat. 125:1-15) original method, with modifications by Pagel (1992; J. theor. Biol. 156:431-442) for dealing with incompletely-resolved phylogenies.

CAIC tests for statistical associations between two or more characters that have been measured for each of a number of clades (which may be populations, species, or higher taxa). It can be used to address questions like:



Obtaining the software: Caic can be obtained from the Caic v2.0 WWW Site or by anonymous FTP from ftp://evolve.zps.ox.ac.uk/FTP/packages/CAIC/CAICv2.0.sea. hqx

Internet information: Caic v2.0 WWW Site

CLADOS

by Kevin Nixon

COMPARE

by Emilia P. Martins

Version: 1.0b

Computer Requirements: COMPARE will eventually run on DOS/Windows, UNIX and Macintosh computers. The C source code is also provided and can be compiled on almost anything else.

Description: COMPARE includes various programs for conducting statistical analyses of comparative data in a phylogenetic context. At the moment, it includes programs to conduct Felsenstein contrasts, spatial autocorrelation analyses, generate random data, trees and/or branch lengths, and various other small things. New programs will be added as they are ready.

Obtaining the software: You can download executables, source code and/or documentation for free from COMPARE's WWW site or via anonymous ftp to work.uoregon.edu (in /pub/COMPARE).

Internet information: Check out COMPARE's WWW site.

MacClade

by Wayne P. Maddison and David R. Maddison

Version: 3.05

Computer Requirements: MacClade requires a Macintosh Plus or later computer (that is, any Macintosh produced since 1987), and System 4.2 or later. The amount of RAM you need depends upon your system and on your analysis, but 1.5 Mb for MacClade is sufficient for most analyses. A full installation requires 2 Mb of hard disk space.

Description: MacClade is a program for analyzing character evolution on phylogenies. It has a graphical spreadsheet editor for entering and editing data matrices, a tree window for viewing and manipulating trees, charting facilities, and so on. A more complete description is given in MacClade's WWW site.

Obtaining the software: Available in North America from Sinauer Associates, 23 Plumtree Road, Sunderland, MA 01375-0407, U.S.A. (413) 549-4300, e-mail: biology@sinauer.com. For information about the distributors elsewhere in the world, contact Sinauer Associates.

Internet information: Check out MacClade's WWW site for more information. This site includes updaters, bug lists, etc. Technical support for MacClade can be obtained by sending electronic mail messages to clade@arizona.edu.

COMPONENT

by Roderic D. M. Page

Version: 2.0

Computer Requirements: COMPONENT requires an IBM PC or compatible running Microsoft Windows 3.0 or later, and at least 2 Mb of RAM. Installation requires about 1 Mb of disk space.

Description: COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography. It features a user-friendly Microsoft Windows interface, WYSIWYG tree printing, interactive tree editor, and online context sensitive help. COMPONENT supports standard tree files (e.g., NEXUS, Hennig86, PHYLIP) and can be used to compute consensus trees, various tree comparison measures, reconciled trees and can generate a range of random trees.

Obtaining the software: COMPONENT can be ordered from this address: COMPONENT, c/- Department of Botany, The Natural History Museum, Cromwell Road, London SW7 5BD, UK. Order forms can be obtained from the author (rod.page@zoology.oxford.ac.uk) or from COMPONENT's WWW site. Cost is 40 Pounds (about $US 60).

Internet information: Check out COMPONENT's WWW site.

STATGEOM

by Kay Nieselt-Struwe

Computer Requirements: Either UNIX workstation or PC running under Linux or PC running under MSDOS using a standard ANSI C-compiler and maybe also Macintosh with a standard ANSI C-compiler.

Description: STATGEOM is a program package for computing the statistical geometry of a set of sequences, addressing hereby the question of the tree-likeness of the set. 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. STATGEOM is an easy-to-use, completely menu-driven software package written in standard ANSI C. Postscript files of the graphs of the statistical geometry are automatically generated. There are many more facilities, among them the possibility to determine the rates of transitions and transversions. Along with the package comes a complete and detailed description of the package as well as an introduction to the method of statistical geometry itself. A publication of the package is under preparation.

Obtaining the software: STATGEOM can be obtained by anonymous ftp from cage.mpibpc.gwdg.de in directory /pub/kniesel. The file is called statgeom.tar.gz and is a (GNU-)compressed tar file.

TreeMap

by Roderic D. M. Page

Version: 1.0

Computer Requirements: Either a Macintosh running System 7.0 or later, or a Windows PC running Microsoft Windows 3.1 or later.

Description: Experimental program for comparing host and parasite phylogenies. Reads PHYLIP and PAUP tree files, and data COMPONENT files. Program comes with example data files and documentation in Postscript. The versions for the Mac and for Windows are essentially identical.

Obtaining the software: TreeMap can be obtained from TreeMap's WWW site.

Internet information: Check out TreeMap's WWW site.

Treeview

by Roderic D. M. Page

Version: 0.95

Computer Requirements: TreeView requires either a Macintosh or Power Macintosh running System 7.0 or later, or an IBM PC compatible running Windows 3.1 or later.

Description: TreeView is a program for displaying NEXUS and PHYLIP format trees, and has the following features:


Obtaining the software: TreeView can be obtained from the TreeView WWW site.

Internet information: TreeView WWW site.