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Web or e-mail servers that can analyze data for you
This list gives only a brief description of each service.
Congratulations to these
groups for providing these free services.
have made available servers using PHYLIP:
- GeneBee group of the Belozersky Institute, Moscow State University, Russia. Results
are returned by email.
- The Computational Biochemistry Group of the ETH
in Zürich, Switzerland has five programs available on
its Darwin server, which returns
results by email:
- TreeGen, which
uses a distance matrix method with distance matrix that you supply,
- AllAll, which
does a multiple alignment of protein sequences and can either compute a
distance matrix or rooted or unrooted phylogenies using a distance method.
- PhylogeneticTree computes either a parsimony tree or a distance method
that bases itself on a matrix obtained from all pairwise alignment scores
among a set of sequences.
The European Bioinformatics Institite (EBI)
has available a server
for ClustalW .
tree-based multiple alignment runs.
This also produces tree files in Clustal's own format or in PHYLIP format.
The Institut Pasteur in Paris has made
available its Mobyle server with many phylogeny programs. It is available
through its web page
- The Institut Pasteur, Paris has
a server for 15 of the PHYLIP 3.6a programs.
- The Bioinformatics Centre at the University of Wageningen, Netherlands,
makes available a server for the DRAWTREE and DRAWGRAM programs.
- The Spanish EMBNET node
at the Centro Nacional de Biotecnologia, Madrid, makes
the version 3.5c Protpars and Dnapars programs available as a server.
- The Department of Molecular Evolution of the Evolutionary Biology Centre,
Uppsala University, Uppsala, Sweden, makes a web server of 9 PHYLIP 3.5c programs available.
- The Biology Workbench of the San Diego Supercomputer Center makes
available some of the PHYLIP 3.5c programs as a web server, requiring only a
At present it includes web servers for programs from
To find these expand the "phylogeny" tab on their list of programs.
for the ROSE program which
simulates the evolution of DNA, RNA, or proteins sequences with insertions
and deletions is available from the Technische Fakultät of the University of
Bielefeld, Germany at
The INRA in Toulouse, France, has
for Florence Corpet's MultAlin multiple sequence alignment method which is similar
to progressive alignment. It clusters by UPGMA. A "cluster file" is provided which may contain
information on the phylogeny.
Andrew Marriott and John Wetherall at the
Curtin University of Technology, Australia, have made available
a web server
running Michel Raymond and François Rousset's program
Genepop, version 3.4. This can
do many kinds of population genetic analysis -- the relevant feature for
our purposes is the ability to calculate measures of population
Kim Fisker and Thomas Christensen of the
Department of Computer Science, University of Aarhus, Denmark have
for the program RecPars which infers trees with recombination for a set of DNA sequences.
Christian Zmasek and Sean Eddy have made available at
the Howard Hughes Medical Institute Janelia Farms campus a server for their RIO
(Resampled Inference of Orthologs) program from their Forester package. It searches for orthologs of a given
sequence in the PFAM databse.
Don Gilbert of the Department of Biology, University of Indiana has made
available a web server for his Phylodendron tree-drawing Java package, which uses tree drawing programs from
Rishabh Bhandari of Delhi, India has
a web server for a number
of methods for fitting a tree to distance matrix data by combining nodes whose
variance of distances to other nodes are least. It also can calculate
distances between trees and patristic distances from trees.
Sergei Kosakovsky Pond and Simon Frost of the
Antiviral Research Center at the University of California, San Diego, have
the Datamonkey Adaptive Evolution Server which carries out several methods
for detecting positively selected sites in DNA sequences.
The Los Alamos National Laboratory's Hepatitis C
Virus database project has a Findmodel web server
that uses weighbor and
PAML together with methods from
Modeltest to quickly evaluate
a set of models for sequence evolution.
from Arlin Stoltzfus's group at NIST and
Wei Gang Qiu's group at Hunter College that allows manipulation of NEXUS files
containing molecular data sets and trees to modify them, and to print out
data sets and plot trees with various kinds of information highlighted.
The ProtTest server from David Posada's
group in Vigo, Spain that makes available their protein substitution
model selection program ProtTest.
The Hepatitis C Virus database project at Los Alamos National Laboratory, New Mexico
has a server that converts your sequences to PHYLIP format and then gets
DNA distances using PHYLIP and a Neighbor-Joining tree using QuickTree.
for the Java-based multiple-computer likelihood program
MultiPhyl and for the
model selection program ModelGenerator,
from the National University of Ireland, Maynooth.
MrBayes form server creates simple command blocks for the program MrBayes.
sequences from a database and make a tree from them.
ModelTest server runs the ModelTest program for choosing among
models of evolution.
Phylemon web server at the Centro de
Investigacion Principe Felipe in Valencia, Spain can carry out analyses with a
wide variety of phylogeny programs.
MAFFT server is a fast tree-alignment server that uses Fast Fourier Transform methods.
Its program is also in distribution.
finds alignments and trees for protein sequences using HMMM methods.
Phyfi server draws images of phylogenies.
ConSurf server identifies functionally important regions on the
surface of a protein of known three-dimensional structure,
using the phylogeny of it and its close sequence homologues.
(PhylOgenetic WEb Repeater) is a server and the Institute of Information
Sciences in Taiwan using PHYLIP and ClustalW to align sequences and infer
A web server for the
T-REX program which includes
inference of reticulated trees, and has additional tree
construction methods using PHYLIP
programs is available from the T-REX group at the
Université du Québec à Montréal.
The phylogeny.fr server at
the LIRMM and the IGS
in Montpellier, France uses several alignment programs, some
programs for distances and tree-drawing from PHYLIP, and the
to provide a web server that is intended as simple and easy to use.
A slightly earlier set of servers from the LIRMM
for some of these programs is here:
server for the fast
likelihood program RAxML at the
Swiss Institute of Bioinformatics.
server for the MGR
capability of the GRIMM program
to infer distances or phylogenies by minimizing genome rearrangements.
for the Rosette Plotting Tool program that
produces circular tree plots that show the values of characters graphically.
The SWAMI "next generation
biology workbench" server at San Diego Supercomputer Center runs ClustalW, many programs from PHYLIP, and PHYML as
well as doing many kinds of sequence search. Requires free login.
The Malaysian Genomics Resource Center's synatree server allows
you to choose sequences from sequenced genomes and/or upload sequences, and
make Neighbor-Joining, UPGMA, WPGMA or Splitstree trees from them.
The web servers
REFGEN (REFormat GEne Names for phylogenies)
TREENAMER from the Centre for Eukaryotic
Evolutionary Microbiology at the University of Exeter, U.K. replace sequence
reference names in FASTA files with arbitrary identifiers, and replace the
identifiers in treefiles produced from these sequences with the original
server from the Museum of Natural History in Paris computes a measure of congruence between trees that includes a P-value
for the test that the trees are significantly similar.
The PhyloPars server at the
Department of Theoretical Biology of the Vrije Universiteit Amsterdam
estimates ancestral and present day trait values from
incomplete data using a Brownian Motion statistical model (not parsimony).
web server from the School of
Computer Science at McGill University in Montréal, Québec
runs the FootPrinter program
which searches for control sequences near a set of genes using a parsimony
from the Department of Computer Science and Engineering of the University
is a web server which is a front end to the FootPrinter phylogenetic footprinting program.
which will find related prokaryotice genomes containing genes homologous to
the input sequence and run FootPrinter on that data set.
University of Oslo Bioportal web
server makes available (to academic users for a free registration) many different phylogeny
server at the University of Bielefeld, Germany, reconstructs on a given
tree using conserved intervals the ancestral gene orders for the interior
nodes of the tree.
server at the University of Bielefeld, Germany, reconstructs ancestral gene
clusters at interior nodes of a given tree by minimizing gains and losses.
The NetTest server at the Department of Biochemistry,
Genetics and Immunology of the University of Vigo, Spain
characterizes explicit phylogenetic networks into theoretical classes:
Tree, Galled, Tree-Child, and Tree-Sibling.
A web server that configures your data
to enable the files to be run in your own copy of the biogeography
program Lagrange is available in Rick
Ree's lab at the Field Museum of Natural History in Chicago here.
The PhyloExplorer web server that uploads tree
files and manage the collection, including associating Wikimedia images of
species with the tips of the trees, calculation of tree shape statistics, and
identification of relevant trees in the TreeBase database, is available at
its web site at the Institut des Sciences de l'Evolution at the
Université de Montpellier II, France.
The PhyDesign server from Francesc Lopez-Giraldez and Jeffrey P. Townsend of the Department of Ecology and Evolutionary Biology
of Yale University implements the Townsend phylogenetic informativeness profiling, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. It is available at its web site at the Townsend lab.
There are three major collections of older biology software available for
transfer by ftp. Until about 1998 these collected many of the
freely available phylogeny programs and redistributed them. They have
been updated very little since then, partly because many program
authors could distribute programs through their own web sites.
They are thus of historical interest and for access to old programs.
These three archives originally contained almost the same programs, but they
diverged some after 1996, and then after 1998 almost entirely ceased being
- the IUBio archive maintained by Don Gilbert at the Biology Department
of the University of Indiana. Its ftp address is
ftp.bio.indiana.edu. There is also a web page
http://ftp.bio.indiana.edu/software/. It includes a
keyword search capability.
Relevant code will be found in directories:
and also in machine-specific directories
where binaries and sources specific to those families of machines are to be
molbio in subdirectories
evolve for phylogeny software,
align for alignment software
The general IUBIO site can be
http://ftp.bio.indiana.edu It mentions
descriptive list of the software that was available on the IUBio server
as of 1998 which can be found at http://iubio.bio.indiana.edu/soft/molbio/Listings.html. Unfortunately, the links on that page are not active but
must be copied out by hand.
- the EBI software archive at the European Bioinformatics Institute
Cambridge, England (
ftp.ebi.ac.uk in directory
- the Pasteur Institute archive in Paris (
ftp.pasteur.fr in directory
The molbio part of the Indiana IUBio
archive is mirrored (exact copies are maintained) in a number of countries
(I do not know how current these mirrors are):
- A mirror of the
molbio section is maintained at
- A mirror of the molbio section is maintained at
ftp.pasteur.fr in directory
- A mirror of the
molbio section is maintained at
ftp.funet.fi in directory
(This is the end of the software listings).
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Notices added in compliance with University of Washington
requirements for web sites hosted at the University: