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• GeneBee group of the Belozersky Institute, Moscow State University, Russia. Distance matrix analysis from protein or nucleotide sequences.
• The Computational Biochemistry Group of the ETH in Zürich, Switzerland has three programs available on its server:
  • TreeGen, which uses a distance matrix method with distance matrix that you supply,
  • AllAll, which can either compute a PAM matrix from protein sequences or rooted or unrooted phylogenies using a distance method, and
  • Darwin, an environment which has available within it distance matrix methods and split decomposition methods for phylogenies. Darwin is also available for distribution.
  • MultAlign a multiple-sequence alignment program that includes not only alignment but also several distance matrix methods for inferring trees.
• Phyltree, a Java applet that generates a random tree, a distance matrix for it, and uses clustering methods to estimate and display the resulting tree and the true one. From David Joyce of the Computer Science Department at Clark University, Worcester, Massachusetts.
• The Suggest Tree function of the old web page of the Ribosomal Database Project at the University of Illinois (the main project has now moved to Michigan State University but so far has not yet implemented this server on its web page there). You submit a large- or small-subunit ribosomal RNA sequence and this server will align it with their database of sequences, place it in the best position it can on the tree of those sequences, and return the nearby part of that tree.
• A server at the Forschungsschwerpunkt Mathematisierung at the University of Bielefeld, Germany, that runs the SplitsTree 2 program. You paste in a lower-triangular distance matrix, or one in the Nexus format, and it returns the results as a file stored on your system. SplitsTree versions 1 and 2 are also available by ftp.
• Three groups have made available servers using PHYLIP:
  1. The Internet Bioinformatics Group of the Internet Research and Development Unit of the National University of Singapore has a server at http://sdmc.krdl.org.sg:8080/~lxzhang/phylip/.
  2. The Institut Pasteur, Paris has a server at http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html
  3. Joaquin Dopazo at the Centro Nacional de Biotecnologia, Madrid, Spain has made a server available.
• The Ribosomal Database Project at Michigan State University has a server (located at http://www.cme.msu.edu/RDP/html/analyses.html that takes uploaded sequences of either large or small subunit ribosomal RNA, aligns them against its existing database of ribosomal RNA sequences, and can provide a similarity matrix between them. This is related to a distance matrix, but is not corrected for superimposed changes.
• David Robertson (david@igs.cnrs-mrs.fr) of the CNRS in Marseille has implemented TREE and FRAG_TREE, Neighbor-Joining servers that take a ClustalW .ALN file of aligned sequences, use ClustalW to align them and my program DRAWTREE to draw the resulting tree. TREE does the whole alignment, and FRAG_TREE a specified region of the alignment. The TREE server will be found at http://193.50.234.246/~beaudoin/anrs/Tree.html and the FRAG_TREE server will be found at http://193.50.234.246/~beaudoin/anrs/Frag.html.
• 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 a server with many phylogeny programs. It is available through its web page in English at http://bioweb.pasteur.fr/seqanal/phylogeny/intro-uk.html, or its web page in French at http://bioweb.pasteur.fr/seqanal/phylogeny/intro.html. At present it includes web servers for
  • PHYLIP
  • fastDNAml
  • MOLPHY
  • BIONJ
  • TREE-PUZZLE
  • Seq-Gen
  • TreeAlign
  • QR2
  • PhyloQuart
  • LVB
  • BAMBE
• 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 Fakultat 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.
• The Section of Molecular Evolution of the Institute of Cytology and Genetics in Novosibirsk, Russia has a server at http://molevol.bionet.nsc.ru/www_vs.htm for the VOSTORG package. The server can compute distances and find UPGMA, WPGMA, or Neighbor-Joining phylogenies.
• Allen Rodrigo of the Computational and Evolutionary Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand has a server which runs sUPGMA (Serial sample UPGMA). It reconstructs evolutionary histories/genealogies from distance matrices under the assumption of a molecular clock when sequences are obtained serially in time. It can also carry out UPGMA and WPGMA clustering as well as Neighbor-Joining. The Java code for sUPGMA is also available.
• Emília Martins of the Department of Biology, University of Oregon, Eugene, Oregon has made available a server for her program COMPARE using Java. It carries out comparative methods analysis.

• 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/.
  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
  A list of the software on the IUBio server can be found at http://iubio.bio.indiana.edu/soft/molbio/Listings.html. The links on that page are unfortunately 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 Indiana IUBio archive is mirrored (exact copies are maintained) in a number of countries:

Japan

• a full mirror is maintained at ftp.gdbnet.ad.jp in directory ftpsync/ftp.bio.indiana.edu
• a mirror of the molbio section only is maintained at ftp.nig.ac.jp in directory pub/mirror/IUBIO/molbio

Finland

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

Sweden

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

Spain

A mirror of the molbio section is maintained at ftp.uam.es at pub/mirror/molbio

Israel

A mirror of the search, unix, ibmpc, mac, and vax subdirectories of the molbio section is maintained at bioinformatics.weizmann.ac.il in directory pub/software

France

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

U.K.

A mirror of the molbio section is maintained at http://mic3.hensa.ac.uk/hosts/iubio.bio.indiana.edu/molbio/.

India

A mirror of the molbio section is available at imtech.chd.nic.in in directory /pub/mirror_sites/iubio/

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