ABCC : Application's document Page

PHYLIP

3.5

Phylogenetic Analysis, Bioinformatics

Joe Felsenstein
University of Washington
joe@genetics.washington.edu

PHYLIP (the PHYLogeny Inference Package) is a package of programs
for inferring phylogenies (evolutionary trees). Methods that are
available in the package include parsimony, distance matrix, and
likelihood methods, including bootstrapping and consensus trees.
Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters. 

The programs are controlled through a menu, which asks the users
which options they want to set, and allows them to start the
computation. The data are read into the program from a text file,
which the user can prepare using any word processor or text editor.
Some sequence analysis programs such as alignment programs can write
data files in the PHYLIP format. 

Output is written onto special files with names like "outfile" and
"treefile". Trees written onto "treefile" are in the Newick format,
an informal standard agreed to in 1986 by authors of a number of
major phylogeny packages. 

SGI 

/usr/local/fbscapp/phylip 

Account on ABCC's SGI computer systems is required.
To use PHYLIP (assuming C-Shell):
  set path = ($path /usr/local/fbscapp/phylip/exe)
followed by the name of PHYLIP's executable.
Note, that we have SGI optimized serial (i.e., not
parallel) executables for three PHYLIP's programs dnaml,
dnamlk, and dnapars. These executables are as much as 4
times faster than 'regular' PHYLIP executables. In
addition, there is a SGI parallel version of protpars.
To use this executable in parallel set the variables
  setenv OMP_NUM_THREADS number_of_cpus
  setenv MPC_GANG off
All SGI executables are denoted with an .sgi name
extension, i.e., dnaml.sgi, dnamlk.sgi, dnapars.sgi, and
protpars_mp.sgi.   

Text files at /usr/local/fbscapp/phylip/doc.
Check also FAQ on the PHYLIP's web site. 

Bob Stephens
301-8465787
bobs@ncifcrf.gov 

miaskiew

2002-05-28

miaskiew

2002-05-28