PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. Written by Joe Felsenstein of the Department of Genetics at the University of Washington, the PHYLIP package is widely used for phylogenetic analysis. Using PHYLIP release 3.64 which came out 7/15/05.

This package is on the web for UCSF users. There will be two levels of programs. Simple will be the easiest. Advanced will provide greater option selection.

[This is a beta test version. Not all the checks have been installed yet. Please read the disclaimer page prior to running any of the programs. Report all problems to Susan Johns (johns@cgl.ucsf.edu).]

Internet Explorer users: Internet Explorer ignores blank lines when copying text. This trait causes web processes to fail when a user uses the output of one web process as the input to another. When this happens, switch to some other browser that doesn't behave this way.

Currently available programs:

programs for molecular sequence data: program descriptions

• dna
  
  dnadist simple and advanced, documentation
  dnapars simple and advanced, documentation

• proteins
  
  protdist simple and advanced, documentation
  protpars simple and advanced, documentation

• flow combinations
  
  (created distance data then run either fitch or neighbor and display the tree)
  
  
  protdist simple and advanced
  dnadist simple and advanced

programs for distance matrix data: program descriptions

neighbor simple and advanced, documentation
fitch simple and advanced, documentation
kitsch simple and advanced, documentation

others:

seqboot simple and advanced, documentation
drawgram simple and advanced, documentation
drawtree simple and advanced, documentation

Last updated 8/3/05