To previous part of Software pages

• GeneBee group of the Belozersky Institute, Moscow State University, Russia. Results are returned by email.
  • Distance matrix analysis from protein or nucleotide sequences using the Treetop program.
  • Server for alignment and neighbor-joining trees using the ClustalW program.
• 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.
• Five groups have made available servers using PHYLIP:
  • 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 free registration.
• 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 at http://mobyle.pasteur.fr/cgi-bin/portal.py. At present it includes web servers for programs from

  BAMBE PHYLIP BIONJ

  QuickTree weighbor fastDNAml

  PHYML TREE-PUZZLE Seq-Gen

  LVB TreeAlign TipDate

  NJplot EMBOSS Distmat Ktreedist

  To find these expand the "phylogeny" tab on their list of programs.
• A server 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 http://bibiserv.TechFak.Uni-Bielefeld.de/rose/.
• The INRA in Toulouse, France, has a server 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 differentiation.
• Kim Fisker and Thomas Christensen of the Department of Computer Science, University of Aarhus, Denmark have made available a server 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 PHYLIP.
• 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.
• Nexplorer a server 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. various
• 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.
• The MultiPhyl and ModelGenerator server 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.
• The 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.
• SATCHMO-JS server 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.
• POWER (PhylOgenetic WEb Repeater) is a server and the Institute of Information Sciences in Taiwan using PHYLIP and ClustalW to align sequences and infer phylogenies.
• 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 programs

  PhyML TNT BIONJ

  MrBayes DTscore TreeDyn

  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:
  • PHYML
  • FastME
  • PhySIC
  • PhySIC_IST
• A server for the fast likelihood program RAxML at the Swiss Institute of Bioinformatics.
• A server for the MGR capability of the GRIMM program to infer distances or phylogenies by minimizing genome rearrangements.
• A server 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) and 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 species names.
• Icong 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).
• A 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 criterion,
• MicroFootPrinter from the Department of Computer Science and Engineering of the University of Washington 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 programs including:

  BEAST GARLI MAFFT ModelTest

  MrBayes MrModeltest PAML

  PAUP* PhyloBayes PHYML

  ProtTest RAxML Treefinder

• The Roci 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.
• The Rococo 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.

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• 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 at http://ftp.bio.indiana.edu/software/. It includes a keyword search capability.
  Relevant code will be found in directories:
  • molbio in subdirectories
    • evolve for phylogeny software,
    • align for alignment software
  • and biology.
  and also in machine-specific directories where binaries and sources specific to those families of machines are to be found:
  • unix,
  • ibmpc,
  • mac,
  • vax, and
  • java
  The general IUBIO site can be found at http://ftp.bio.indiana.edu It mentions a 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 pub/software), and

• the Pasteur Institute archive in Paris (ftp.pasteur.fr in directory pub/GenSoft/).

Mirrors

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):

Sweden

A mirror of the molbio section is maintained at ftp.sunet.se in directory pub/molbio

France

A mirror of the molbio section is maintained at ftp.pasteur.fr in directory /pub/GenSoft/mirrors/IUBio/molbio.

Finland

A mirror of the molbio section is maintained at ftp.funet.fi in directory pub/sci/molbio/iumolbio

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