Phylogeny Programs

★ wanayoo — archive 1999 http://evolution.genetics.washington.edu/phylip/software.html

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Here are some 175 of the phylogeny packages, and 17 free servers, that I know about. Some of them are available over Internet from ftp server machines, or by World Wide Web.

The programs listed below include both free and non-free ones; in some cases I do not know whether a program is free. I have listed as free those that I knew were free; for the others you have to ask their distributor.

If you discover any inaccuracies, or feel that I have left any important programs or facts out, or if links do not work properly, please e-mail me (joe@genetics.washington.edu).

List of packages arranged ...

... by methods available

... by computer systems on which they work

... cross-referenced by method and by computer system.

... to show the most recent listings

... to show ones most recently changed

Phylogeny programs formerly listed here but no longer distributed

Which kinds of programs are and are not listed

Other lists of phylogeny software

Table of contents by methods available

General-purpose packages
Parsimony programs
Distance matrix methods
Computation of distances
Maximum likelihood and related methods
Quartets methods
Artificial-intelligence methods
Invariants (or Evolutionary Parsimony) methods
Interactive tree manipulation
Looking for hybridization or recombination events
Bootstrapping and other measures of support
Compatibility analysis
Consensus trees and distances between trees
Tree-based alignment
Biogeographic analysis and host-parasite comparison
Comparative method analysis
Simulation of trees or data
Examination of shapes of trees
Clocks, dating and stratigraphy
Description or prediction of data from trees
Tree plotting/drawing
Sequence management/job submission
Teaching about phylogenies
Web or e-mail servers that can analyze data for you

General-purpose packages

Parsimony programs

Distance matrix methods

PHYLIP
PAUP*
MEGA
MacT
ODEN
Fitch programs
ABLE
TREECON
DISPAN
RESTSITE
NTSYSpc
METREE
TreePack
TreeTree
GDA
Hadtree, Prepare and Trees
Wisconsin Sequence Analysis Package (GCG)
SeqPup
PHYLTEST
Lintre
WET
Phylo_win
njbafd
Gambit

gmaes
DENDRON
Molecular Analyst Fingerprinting
BIONJ
TFPGA
MVSP
SOTA
ARB
BIOSYS-2
Darwin
T-REX
sendbs
nneighbor
DAMBE
weighbor
QR2
DNASIS
minspnet
sUPGMA
PAL
Arlequin

Computation of distances

PHYLIP
PAUP*
RAPDistance
MULTICOMP
MARKOV
RSVP
Microsat
DIPLOMO
OSA
DISPAN
RESTSITE
NTSYSpc
TREE-PUZZLE
Hadtree, Prepare and Trees
Wisconsin Sequence Analysis Package (GCG)
AMP
GCUA
DERANGE2
POPGENE

TFPGA
REAP
MVSP
SOTA
RSTCALC
Genetix
BIOSYS-2
RAPD-PCR package
DISTANCE
Darwin
sendbs
K2WuLi
GeneStrut
Arlequin
DAMBE
DnaSP
PAML
puzzleboot
MATRIX
PAL

Maximum likelihood and related methods

Quartets methods

Artificial-intelligence methods

SOTA

Invariants (or Evolutionary Parsimony) methods

Interactive tree manipulation

Looking for hybridization or recombination events

Bootstrapping and other measures of support

Compatibility analysis

Consensus trees and distances between trees

Tree-based sequence alignment

Biogeographic analysis and host-parasite comparison

Comparative method analysis

Simulation of trees or data

Examination of shapes of trees

Clocks, dating and stratigraphy

Description or prediction of data from trees

Tree plotting/drawing

Sequence management/job submission

Teaching about phylogenies

Phylogenetic Investigator

Table of contents by computer systems
on which they work

Unix (source code in C or executables)

PC's

... under Windows

... under DOS or in a Windows "DOS box"

Macintoshes or PowerMacs

VMS executables or C sources with VMS compilation support

e-mail or Web servers that can analyze data for you

Unix (source code in C or executables). I have included programs that are available as C source code because most Unix workstations have a C compiler. (A few programs with FORTRAN source code are included too).

PC's

as Windows executables (not counting executing in a "DOS box")

under DOS (MSDOS, PCDOS) or in a Windows "DOS box"

Macintosh or PowerMac executables

VMS executables or C sources with VMS compilation support. (Many of the programs listed under Unix above have C source code which can also be compiled under VMS).

Recent listings

Here are the packages that have most recently been added to these listings: (the most recent ones first). Entries are retained in this list for 3 months.

UO (20 April 2000)
Gambit (18 April 2000)
Network (13 April 2000)
TreeEdit (5 April 2000)
dnarates (31 March 2000)
Phylogenetic Independence (29 March 2000)
DNASEP (18 March 2000)
SEPAL (18 March 2000)
Mavric (6 March 2000)
RadCon (26 February 2000)

Recent changes

Here are the packages whose entries have most recently been changed: The date on which each change was entered is shown. Entries are retained in this list for 3 months. (Note that changes may be as small as updated version numbers). The most recent changes are first.

Arlequin (24 April 2000)
puzzleboot (23 April 2000)
TREE-PUZZLE (23 April 2000)
RASA (23 April 2000)
ClustalW (18 April 2000)
CLINCH (17 April 2000)
Fels-Rand (16 April 2000)
PAL (14 April 2000)
TurboTree (13 April 2000)
Hadtree, Prepare and Trees (13 April 2000)
weighbor (13 April 2000)
ProSeq (13 April 2000)
Microsat (11 April 2000)
njbafd (4 April 2000)
Lintre (4 April 2000)
sendbs (4 April 2000)
gmaes (4 April 2000)
Nona (15 March 2000)
SECANT (15 March 2000)
TipDate (10 March 2000)
NTSYSpc (28 February 2000)

Other lists of phylogeny software

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.
The BioCatalog phylogeny page at the European Bioinformatics Institute, located at http://corba.ebi.ac.uk/Biocatalog/Phylogeny.html
The Institut Pasteur in Paris has the Bio NetBook, a search facility for biocomputing resources. It is located at http://www.pasteur.fr/recherche/BNB/bnb-en.html. Programs for phylogenies can be found by, for example, selecting software from the Resource Type list and evolution from the Biological Domain list without selecting any Organism.
A brief list of programs at the Willi Hennig Society's home pages. It reflects a rather different worldview, centered on the parsimony method.
Classification and clustering programs available for free by network are described in a useful Web page from the Classification Society of North America at http://www.pitt.edu/~csna/software.html. Note, however, that inferring phylogenies and making clusters are different tasks; the software described on that list will be of most use to people who are trying to cluster or classify but not to infer phylogenies.
Genamics, a company located in Hamilton, New Zealand, maintains the SoftwareSeek searchable index of bioinformatics software at http://genamics.com/software/index.htm in a number of categories. One of them is Phylogenetic Analysis. They have a reasonably large number of entries under that heading, though it also includes some statistical genetics software that is really not phylogenetic. Their listing has links to the web sites of the software; for those programs that are not available by Web they maintain copies for download at their server.
David Robertson of the Department of Zoology, University of Oxford has a very informative web site at http://grinch.zoo.ox.ac.uk/RAP_links.html listing programs and their web sites that test for the presence of recombination or hybridization events in DNA sequence data. It lists some programs that are covered here, and others that are outside the scope of these web pages.
Georg Fuellen at the University of Bielefeld, Germany, has a very good page on Multiple Alignment Resources at http://www.techfak.uni-bielefeld.de/bcd/Curric/MulAli/welcome.html.
Don Gilbert, of the Department of Biology of the University of Indiana, has a good web page on Free Software in Molecular Biology for Macintosh and MS Windows computers at http://iubio.bio.indiana.edu/soft/molbio/Listings.html. It lists some popular packages and all packages and programs kept at the IUBio ftp server (see our description of that server). Unfortunately the web links on that page are not active so the addresses must be retyped by hand.
Andrea Hansen, of the Universität Braunschweig, Germany, has created the bioinformatik.de index of resources. It includes a list of software located at http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software. The phylogeny programs listings there are located within the categories for different operating systems.
The National Biotechnology Information Facility has a list of phylogeny programs (including some population genetics programs as well) at http://www.nbif.org/software/software.html#phylogenetic_analysis.
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.

To first page of main software listing

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