Version 3.6

The documentation for PHYLIP version 3.6 is distributed in the form of web pages. The latest version

Here are other places where the PHYLIP 3.6 web pages (or 3.61, 3.62, etc.) also available on the web:

• The Center for Scientific Computing, Espoo, Finland.
• The Institut Pasteur, Paris.
• Sequence Analysis Facility, Biology Division, California Institute of Technology, Pasadena, California.
• Molecular Evolution Workshop of the Marine Biological Laboratory, Woods Hole, Massachusetts.
• The Biomolecular Computing Resource of the Medical University of South Carolina (some programs)
• LITBIO Laboratory for Interdisciplinary Technologies in Bioinformatics, at Segrate in Italy.
• The Environmental Genomics Thematic Programme Data Centre in Swindon, U.K.
• PHYLIP documentation is available on the web site of the BIRCH package by Brian Fristensky in the University of Calgary, Alberta, Canada. Some of it is also linked to from a web tutorial on molecular phylogeny there.
• The Bioinformatics Centre at the University of Pune, India as part of an ICGEB course there.

Version 3.5

Quite a few sites formerly made PHYLIP v3.5 documentation available in HTML form. Many have since upgraded to version 3.6. The remaining ones include:

• The Bioinformatics Resource at Stanford University.
• The ICGEBnet in Trieste, Italy.
• Biocomputing, University of Zürich and ETH Zürich.
• Instituto Oswaldo Cruz, Saõ Paulo, Brazil.
• Pittsburgh Supercomputing Center, Pittsburgh, Pennsylvania.
• The Center for Molecular and Biomolecular Informatics of the University of Nijmegen, Netherlands.
• The Bioinformatics Resource of the University of Hong Kong, China.
• Research Computing Resource, New York University School of Medicine.
• Jun Ishikawa of the National Institute of Infectious Diseases, Japan.

Here is some documentation written by others, explaining the use of PHYLIP:

• Jarno Tuimala of the Center for Scientific Computing, Espoo, Finland, has written an excellent primer on the use of PHYLIP. It can be downloaded as a PDF.
• The North Carolina Bioportal at the University of North Carolina in Chapel Hill has their own documentation pages explaining parts of PHYLIP.

The EMBNET has had its Spanish node prepare a brief guide to using PHYLIP v3.5. This is available in a number of forms including:

• A short HTML version.
• A short RTF version (which can be read into Microsoft Word).
• A much bigger (1 Mb) file with a PDF version, which is the same text but made longer by graphic images.

Some sites have also been bold enough to make PHYLIP available on a server basis -- you can submit jobs and they will analyze them and return the results. The ones I am currently aware of are:

version 3.6

• The Institut Pasteur, Paris has a server for many of the PHYLIP 3.6a programs at http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html
• The LITBIO (Laboratory for Interdisciplinary Technologies in Bioinformatics) in Italy makes available a PHYLIP server at Segrate, Italy. It requires a free registration.
• The Bioinformatics Centre at the University of Wageningen, Netherlands, makes available a server for the DRAWTREE and DRAWGRAM programs.

version 3.5c

• The Spanish EMBNET node at the Centro Nacional de Biotecnologia, Madrid, makes the Protpars, Proml, Dnapars, and Dnaml 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 3.5 programs available.

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