As people can see from the dates on the most recent updates of these Phylogeny
Programs pages, I have not had time to keep them up-to-date since 2012. I have
now retired, which gives me more time to do research and to support online
resources. So I have hopes of resuming updates, fixing links, and catching up
with the field of phylogenetic inference.
I hope soon to move these software listings webpages to a Github archive, and invite others to help contribute to them and maintain them.
In the meantime, I may not be able to 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. If anyone else wants to help with this, let me know.
|Methods||By computer||Cross-referenced||Data types||Web servers||New programs||Submitting|
|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 ...|
|Table of contents by methods available|
Distance matrix methods
Computation of distances
Maximum likelihood methods
Bayesian inference 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).
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
Description or prediction of data from trees
Sequence management/job submission
Teaching about phylogenies
Table of contents by computer systems
on which they work
(I am just starting to list interpreter code here. Until recently it was listed under Unix, Windows and/or Mac OS X). Until I finish transferring interpreter code here this list will be incomplete, and you will find many programs written in interpreted languages there).
|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||
(aside from microsatellite loci)
(under construction: more coming soon)
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.
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.
|Other lists of phylogeny software|
http://www.ucmp.berkeley.edu/subway/phylo/phylosoft.html. A few programs are listed, but there is a very nice list of software lists there.
bioinformatik.deindex 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 phylogeny software is under "Phylogenetic Analysis" within each operating system.
http://genamics.com/software/index.htmin 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
|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.
To first page of main software listing