Owing to other pressures on my time, I cannot devote time to searching for new programs, so their authors are begged to (please!) use the submission form instead. That form will be found at the "Submitting" link below. If you are upset that your program is not included, but it's too much trouble for you to fill out the submission form, then I will not listen to you. This list of software is now aging and its links are becoming more and more outdated. I will make attempts to fix them when I can. If anyone else wants to help with this, let me know.

Methods By computer Cross-referenced Data types Web servers New programs Submitting

[Phylip icon] [PAUP* icon] [MacClade icon] [Hennig86 icon] [Random Cladistics icon] [AutoDecay icon] [TREECON icon] [Spectrum icon] [SplitsTree icon] [COMPONENT icon] [TREEMAP icon] [CAIC icon] [TreeView icon] [TreeView X icon here] [DNA Stacks icon] [DendroMaker icon] [CONSERVE icon] [GeneDoc icon] [Seq-Gen icon] [SeqPup icon] [Tree Draw Deck icon]
[Phylodendron icon] [TreeRot icon] [Treevolve icon] [TREE-PUZZLE icon] [PSeq-Gen icon] [GeneTree icon] [SeqPup Java icon] [POPGENE icon] [QDate icon] [TFPGA icon] [PASSML icon] [Genetix icon] [T-REX icon] [NJPlot icon] [Arlequin icon] [DAMBE icon] [DnaSP icon] [Modeltest icon] [CodonBootstrap icon] [DNASIS icon] [BioEdit icon]
[ProSeq icon] [MacroCAIC icon] [PAL icon] [RadCon icon] [PI icon] [TreeEdit icon] [TipDate
icon] [PLATO icon] [TreeExplorer icon] [HY-PHY icon] [Genie icon] [TreeThief icon] [TCS icon] [EDIBLE icon] [Winboot icon] [Mega3 icon] [Mesquite icon] [Phyledit icon] [SYN-TAX icon] [PTP icon]
[Network icon] [PAST icon] PHYLOGENY PROGRAMS [GeneStudio Pro icon] [Treefinder icon]
[ClustalX icon] [Treemap2.0beta icon] [MrBayes icon] [YCDMA icon]
[NSA icon] [BEAST icon] [Tracer icon] [Phylogenetic Investigator icon] [Datamonkey server icon] [SymmeTREE icon] [TreeJuxtaposer icon] [Jevtrace icon] [Spectronet icon] [TNT icon] [CAFCA icon] [Phylogen icon] [Dnatree icon] [ProtTest icon] [GEODIS icon] [TreeScan icon] [TreeMe icon] [Simplot icon] [ProfDist icon] [START icon] [Permute! icon]
[SuperTree icon] [Swaap icon] [Swaap PH icon] [MESA icon] [NimbleTree icon] [ArboDraw icon] [SIMMAP icon] [SGRunner icon] [CBCAnalyzer icon] [Notung icon] [Cadence icon] [TreeMaker icon] [BAli-Phy icon]   [Geneious icon] [Phylemon server icon] [MrEnt icon] [Kakusan4 icon] [MAPPS icon]  [GARLI icon] [TreeStat icon] [FigTree icon]
  [TopD/fMts icon] [LVB icon] [Supertree icon] [Mavric icon] [HyperTree icon] [Dendroscope icon] [Phylocom icon] [phylogeny.fr icon] [TOPALi icon] [ES icon] [GenoDive icon] [swami icon]    [Phyutility icon] [PhyloWidget icon] [Bionumerics icon] [BEST icon] [MANTiS icon] [Synatree icon] [PHASE icon] [UGENE icon] [ETE icon]
[IDEA icon] [DendroPy icon] [Puzzleboot icon] [PhyloQuart icon] [ELW icon] [Cactus-Pie icon] [Cactus-Pie icon] [Cactus-Pie icon] [Cactus-Pie icon] [DAWG icon] [GenGIS icon] [GenGIS icon] [GenGIS icon] [PhyRe icon] [iGTP icon] [Recodon icon] [NetRecodon icon] [GHOSTS icon] [NetTest icon] [raxmlGUI icon] [MixtureTree icon]

Changes Waiting list Other lists Old programs Not listed News

Here are 392 phylogeny packages and 54 free web servers, (almost) all that I know about. It is an attempt to be completely comprehensive. I have not made any attempt to exclude programs that do not meet some standard of quality or importance. Updates to these pages are made roughly monthly. Here is a "waiting list" of new programs waiting to have their full entries constructed. Many of the programs in these pages are available on the web, and some of the older ones are also available from ftp server machines.

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. Usually when I say that a program is downloadable from a web site, this means that it is available free.

Email addresses in these pages have had the @ symbol replaced by (at) and also surrounded by invisible confusing tags and blank characters in hopes of foiling spambots that harvest email addresses.

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 at: (joe (at) gs.washington.edu). You can also use the submission form here to submit new entries.

Owing to past NSF support of these pages, I am required to note that any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation (NSF supported these pages from 1995-2003).

List of packages arranged ...

... by methods available

... by computer systems on which they work

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

... by ones which analyze particular kinds of data.

... 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

New programs waiting to be added


Table of contents by methods available


General-purpose packages

Parsimony programs

Distance matrix methods

Computation of distances

Maximum likelihood methods

Bayesian inference methods

Quartets methods

Artificial-intelligence and genetic algorithms methods

Invariants (or Evolutionary Parsimony) methods

Interactive tree manipulation

Looking for hybridization or recombination events

Bootstrapping and other measures of support (for Bayesian support methods see the Bayesian inference list above).

Compatibility analysis

Consensus trees, subtrees, supertrees, and distances between trees

Tree-based sequence alignment

Gene duplication and genomic analysis

Biogeographic analysis and host-parasite comparison

Comparative method analysis

Simulation of trees or data

Examination of shapes of trees

Clocks, dating and stratigraphy

Model Selection

Description or prediction of data from trees

Tree plotting/drawing

Sequence management/job submission

Teaching about phylogenies


Table of contents by computer systems
on which they work

Unix (source code in C or executables)

Multiplatform interpreters (Java, Perl, Python, R, MATLAB)

PC's

... under Windows

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

Macintoshes (under Mac OS X or Mac OS)

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



Analyzing particular types of data

Here you will find lists of programs that analyze types of data other than molecular sequence data. We will gradually expand this list of data types.

Microsatellite data     RAPDs, RFLPs, or AFLPs     Continuous quantitative    
characters
Gene frequencies
(aside from microsatellite loci)

(under construction: more coming soon)


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 6 months. Note also below the "waiting list" area listing programs that are to be added. You can use the submission form here to submit new entries.

  • (List is currently empty because I have been unable to do much updating owing to other pressures so no new packages have been added in the last year).


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 6 months. (Note that changes may be as small as updated version numbers or a modified web address). The most recent changes are first.

  • LVB (19 June 2014)


Other lists of phylogeny software

  • 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 as of 1998 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 at that time (see our description of that server). Unfortunately the web links on that page are not active so the addresses must be copied out and pasted into the URL box of your browser.
  • 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. Unfortunately, the links to the software are very out of date and few of them work.


    New programs waiting to be added

    This is a "waiting list" showing links to the web pages of many new phylogeny programs, which I have not yet had time to add to the main listing. They will be listed there, with a single web link and no detailed explanation. I hope that this list will gradually shrink as the new programs are put into the main listing. You can use the submission form here to submit new entries.

    These are waiting to be added:

    This bunch are all old programs from Masatoshi Nei's lab, available from the same web page there

    These are not from the Nei site: I will be adding new programs as they come in, and removing programs from this waiting list as they are added to the main listing. You can speed up the listing of a program and help me by using the submission form here to submit entries. Any entries submitted that way (including ones that are already in the Waiting List) will "jump the queue" and get highest priority for being added to the full listing.


    News

    Mysteries you can help us solve

    These haven't been entered because I am not sure what they do and whether it is covered by this list. Anyone with relevant information should let me know.

          Until I get more information these programs cannot be further listed.


    To first page of main software listing


    [Phylip icon here] ... to the PHYLIP home page

    Notices added in compliance with University of Washington requirements for web sites hosted at the University:      Privacy     Terms