| 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 ... |
Phylogeny programs formerly listed here but no longer distributed
| Table of contents by methods available |
General-purpose packages
- PHYLIP
- PAUP*
- MEGA
- Phylo_win
- ARB
- DAMBE
- PAL
- Bionumerics
- Mesquite
- PaupUp
- BIRCH
- Bosque
- EMBOSS
- phangorn
- Bio++
- ETE
- DendroPy
- SeaView
- Crux
Parsimony programs
Distance matrix methods
Computation of distances
Maximum likelihood methods
Bayesian inference methods
Quartets methods
- TREE-PUZZLE
- SplitsTree
- PHYLTEST
- GEOMETRY
- PICA
- Darwin
- PhyloQuart
- Willson quartets programs
- Gambit
- IQPNNI
- STC
- Quartet Suite
- LEVEL2
- Bosque
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
- TreeAlign
- ClustalW
- MALIGN
- GeneDoc
- DAMBE
- POY
- ALIGN
- DNASIS
- FootPrinter
- ALIFRITZ
- T-Coffee
- ArboDraw
- BAli-Phy
- Geneious
- BIRCH
- MAFFT
- LOBSTER
- DART
- MUSCLE
- Bosque
- EMBOSS
- SeaView
- SuiteMSA
Gene duplication and genomic analysis
- DERANGE2
- FORESTER
- BPAnalysis
- Notung
- TopD/fMts
- DTscore
- DART
- gtp
- EvolSimulator
- DTdraw
- Mgenome
- Tree Tracker
- bms_runner
- MANTiS
- ETE
- MANTiS
- iGTP
Biogeographic analysis and host-parasite comparison
- COMPONENT
- TREEMAP
- DIVA
- TreeFitter
- GEODIS
- Tarzan
- ParaFit
- Phylocom
- AxParafit
- GenGIS
- S-DIVA
- Lagrange
- CoRe-PA
- Jane
Comparative method analysis
Simulation of trees or data
Examination of shapes of trees
- MacroCAIC
- Genie
- PAL
- Vanilla
- RadCon
- BRANCHLENGTH
- APE
- Tracer
- SymmeTREE
- TreeScan
- MESA
- apTreeshape
- TreeStat
- CTree
- Phyutility
- laser
- PhyRe
- Bio::Phylo
Clocks, dating and stratigraphy
Model Selection
- Modeltest
- MrMTgui
- MrModeltest
- Porn*
- ModelGenerator
- ProtTest
- MrAIC
- Modelfit
- DT-ModSel
- BayesTraits
- Kakusan4
- MAPPS
- DART
- Concaterpillar
- Statio
- jMODELTEST
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 |
... under Windows
-
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. (Programs in other compiled languages such as FORTRAN and Pascal, and in interpreted languages such as Java, Perl, Python, or R are also included), as are Java executables. For many of these the programs can also be compiled or run on Windows or Mac OS X systems if they have the appropriate compilers or interpreters loaded.
-
Multiplatform interpreters (Java, Perl, Python, R, MATLAB). These are programs that are written in a language that is interpreted, step by step, in real time by a computing environment that can run on many different operating systems.
(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).
Java
-
PC's
- as Windows executables (not
counting executing in a "DOS box"). Programs available as source
code which is Windows-specific are listed here. Java executables
are also included. (Note that compilers available on Windows
systems, particularly the free Cygwin and MinGW compilers, can
also be used to compile many of the programs listed above under
Unix generic source code). Programs run in interpreted
environments such as Perl, Python, R or MATLAB can also be run
under Windows if the proper environment is installed. These
programs are listed above under Unix.
- under DOS (MSDOS, PCDOS) or in a
Command Prompt accessory "DOS box" in Windows
- as Windows executables (not
counting executing in a "DOS box"). Programs available as source
code which is Windows-specific are listed here. Java executables
are also included. (Note that compilers available on Windows
systems, particularly the free Cygwin and MinGW compilers, can
also be used to compile many of the programs listed above under
Unix generic source code). Programs run in interpreted
environments such as Perl, Python, R or MATLAB can also be run
under Windows if the proper environment is installed. These
programs are listed above under Unix.
-
Macintosh Mac OS X or Mac OS executables. Java executables are also included. (Note that most of the programs in the Unix/Linux list above can also be compiled for Mac OS X using the GCC compiler that is distributed with Mac OS X). Programs run in the interpreted environments Perl and Python can also be run in Mac OS X as these are included in the Mac OS X distribution. We have not yet included these in the list below but should. R or MATLAB can also be run under Mac OS X if the proper environment is installed. These programs are listed above under Unix.
| 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.
|
| 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.
|
| Other lists of phylogeny software |
- There is one phylogeny software list even more
complete and up-to-date than this one: a more recent version of this
list. If you are reading this on the web pages at our server
evolution.gs.washington.edu, you are reading the most up-to-date version. But if you are reading a version stored anywhere else, you might want to look here instead. - Sergios-Orestis Kolokotronis has posted an extensive table of phylogeny programs at his site at the American Museum of Natural History, and near it are others under headings such as "molecular evolution" and "alignment".
- Wikipedia has a good list of sequence alignment software (including
both tree-based and non-tree-based alignment methods)
here
at
http://en.wikipedia.org/wiki/List_of_sequence_alignment_software - David Robertson of the Bioinformatics Education and Research at the
University of Manchester, England, maintains a very informative web
site at 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. That
site
is located at
http://bioinf.man.ac.uk/robertson/recombination/programs.shtml. - Mike Robeson at the University of Colorado maintains a page with multiple programs listed as Bioinformatics software for Mac OS X.
- The Bioinformatics Organization, a nonprofit group in Hudson, Massachusetts, has posted the bioinformatics.org web pages. These offer a free membership and host open source software projects in bioinformatics. They also have a Molecular Linux listing of Linux programs to carry out bioinformatics tasks, which can be sorted by keywords.
- On Wikipedia there is a List of phylogenetic tree visualization
software
at
http://en.wikipedia.org/wiki/List_of_phylogenetic_tree_visualization_software - The University of California Museum of Paleontology page of
Phylogenetics Software
Resources
at
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. - Andrea Ramge, of Biomax Informatics AG, Martinsried, Germany has
created the
bioinformatik.deindex of resources. It includes a list of software located athttp://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. - Richard Christen at the Université de Nice, France, has a list of
Tree and Tree-software for visualisation and manipulations dealing
with phylogenetic
trees at
http://bioinfo.unice.fr/biodiv/Tree_editors.html - Silvio Nihei at the University of São Paulo in Brazil has produced a list: Programas para Filogenia in Portugese. It concentrates on a small number of programs that mostly use parsimony methods.
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
- ADAPTSITE, intended to estimate positive and negative selection at a single amino acid site.
These are not from the Nei site:
- PhyRe infers adequacy of taxon sampling for phylogenetic studies.
- phylobase is an R package that contains a class of functions for comparative methods, incorporating one or more trees and trait data.
- PhyML-mixtures, a PhyML version for mixture of amino acid models (EX2, EX3, EHO, UL2, and UL3).
- PhyD*, Fast NJ-like algorithms to deal with incomplete distance matrices.
- SDM a fast distance-based approach for tree and supertree building in phylogenomics.
- SSIMUL does speciation signal extraction from multigene families.
- Clearcut carries out Relaxed Neighbor Joining (RNJ), a faster NJ-like distance method.
- MP-EST (also described here) uses trees from different loci to infer a species tree by a pseudo-maximum-likelihood method.
- TreeRogue, an R script for getting trees from published figures of them.
- Serial NetEvolve simulation program evolves serially-sampled sequences with or without recombination.
- Rococo reconstructs ancestral gene clusters for a multigene family on a given tree.
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 |
- (27 May 2012) Adding one entry from the Waiting List each week, have caught up with submissions submitted through the web form, and am populating a new column in the cross-referenced table, one for multiplatform interpreted code such as Java, Perl, Python, R, and MatLab. The Java programs are entered in that column. After this I will put the others in it, then go back to the main Phylogeny Programs front web page and put in a software category for these interpreters. If you have a new program, or an old one that I don't list, don't wait for me to find it by myself -- I still don't have time to, so use the web submission form.
- (19 March 2012) Well, I should have known that another quarter of teaching lay ahead. Now that is done and I should make gradual progress over the next two quarters.
- (23 December 2011) Once again I got stalled by heavy teaching. Now resuming again and hope to gradually catch up. One puzzle is how to handle R packages. There are a great many of them, and most are not listed here yet. It simply is too much work for me to track them all down, figure out their features, and make an entry for each one. So I will put in only those whose authors use our submission form to help create the entry.
- (20 August 2011) I have resumed adding new submissions that people sent in using our software submission forms -- there are about 10 waiting, some having waited for over 6 months. Apologies for that, I was busy teaching and desperately trying to write up old results. I hope to gradually add all 10 over the next month or so, one at a time.
- (17 December 2010) I have started (on this 107th anniversary of the Wright Brothers' famous first flight) this News section of the page. The current status is that I have completed (over the past 2-3 years) a complete pass through the listings, updating them. However of course some may have become outdated since then. Ahead is adding new entries, of which I expect there to be 30-40. I am caught up on entries that were submitted by the web submission form.
- (19 December 2010) I have finished adding the ones that were already in our Waiting List. Now to take some of the approximately 40 leads that I have accumulated and put entries for the relevant ones into the Waiting List.
- (19 June 2014) Things have been stalled for some years but now I am gradually (and slowly) resuming adding and correcting entries. Please keep using the software submission form, and please be patient. I was stalled owing to needing to write grants, and owing to not getting them so I now have no programming assistance. Progress to being current will be slow. If you are impatient, how about volunteering to help? We could set up some web site accessible to a team.
| 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.
- 3item extracts 3-item statements from "areagrams", whatever that means, but can only be accessed by joining their Yahoo group. So I don't really know what it does.
- Dependency v2.1 uses Multiple Interdependency to detect functional interactions between amino acids in proteins. Does not seem to actually use a phylogeny.
- Codep Maximizes co-evolutionary interdependencies to discover interacting proteins. Also does not seem to actually use a phylogeny.
- PhyloGrapher shows clustering relationships between genes in a genome based on a distance matrix. But is it a phylogeny program?
- Phylosopher commercial package for functional genomics said to include some phylogeny functions. Does it?
- Phylogenator server displaying aligned sequences -- does it actually use or construct phylogenies?
- MultiLocus calculates multiple-locus measures of population differentiation from population genetic data. But unless someone can show me that it can calculate a measure of distance between two populations within a data set, it does not seem appropriate for this list.
- CIPRES-KEPLER Java-based framework for organizing workflow and submitting jobs. I am not sure whether any specifically phylogeny-based pieces have yet been supplied with this.
Until I get more information these programs cannot be further listed.
To first page of main software listing
![[Phylip icon here]](/gvegayon/phylo-software/raw/master/Phylogeny%20Programs_files/PHYLIP.gif)
... to
the PHYLIP home page