Owing to other pressures on my time, I cannot devote much time to searching for
new programs, so their authors are begged to (please!) use the submission form
instead.
|
Here are 367 phylogeny packages and 53 free
web servers, 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 |
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).
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.
- 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 Tool "DOS box" in Windows
- 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)
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.
- FootPrinter server
uses parsimony to search for similar upstream control sequences (18 December
2010)
- MicroFootPrinter server
finds microbial sequences similar to a sequence and runs the FootPrinter web
server on them all (18 December 2010)
- PhyloPars server uses
Brownian Motion models to reconstruct missing data (15 December 2010)
- PhyML-Multi Infers
recombination events using a likelihood criterion (13 December 2010)
- nhPhyML A
local-rearrangements-only version of PHYML for nonhomogenous DNA models (13
December 2010)
- NINJA A fast Neighbor-Joining
program for large numbers of species (6 November 2010)
- Icong web server computing a
measure and test of tree congruence (11 September 2010)
- DendroPy Python library for
phylogenetic computing (7 September 2010)
- PyCogent a Python framework
which
can submit jobs to several phylogeny programs (6 September 2010)
- ETE, a Python programming toolkit
for manipulating trees (8 August 2010)
- REFGEN and TREENAMER web servers
to replace names by identifiers and vice versa (24 July 2010)
- Phybase R package for tree
operations especially for species trees (17 July 2010)
|
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".
- 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
.
It is described as "only updated occasionally"; the most recent links are
about 2006.
- 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
- 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
- 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.
- Silvio Nihei at the University of São Paulo in Brazil has produced
a list: Programas para Filogenia (Morfológica) e Biogeografi in
Portugese. It concentrates on a small number of programs that mostly
use parsimony methods.
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
- GZ-Gamma estimates Gamma parameter of rate variation
- Statio tests stationarity of composition of sequences and tests models
- TIMER
estimates divergence times using a linearized tree approach
- Ancestor
infers ancestral amino acid sequences
- Anc-gene
infers ancestral amino acid sequences when tree is known
- Bn-Bs
estimates synonymous and nonsynonymous distances and then least squares tree
- HON-new
estimates conservative and radical amino acid distances between sequences
These are not from the Nei site:
- PAUPRat
generates a file of commands enabling PAUP* to carry out the “ratchet”
search strategy.
- Archaeopteryx tree
viewer is a successor to ATV which was in the Forester package.
- Crux package of Python
modules for likelihood, Bayesian, and distance methods.
- PhyloExplorer
web server and software to validate, explore and query phylogenies with
regard to a reference taxonomy.
- jModeltest,
a standalone Java replacement for ModelTest
- 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.
- CoRe-PA
reconstructs the coevolutionary history of host-parasite systems using an
event-based method to find cost minimal reconstructions.
- 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.
- (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.
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
... to the PHYLIP home page