PHYLIP - Phylogeny Inference Package (version 3.6)

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
(but it is important that this text file not be in the special format
of that word processor -- it should instead be in "flat ASCII" or
"Text Only" format). Some sequence analysis programs such as alignment
programs can write data files in the PHYLIP format. Most of the
programs look for the data in a file called "infile" -- if they do not
find this file they then ask the user to type in the file name of the
data file.

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.

PHYLIP is the most widely-distributed phylogeny package, and competes
with PAUP to be the one responsible for the largest number of
published trees. PHYLIP has been in distribution since 1980, and has
over 6,000 registered users.

 Joe Felsenstein
 joe@genetics.washington.edu
 Department of Genetics
 University of Washington
 Box 357360
 Seattle, Washington 98195-7360, U.S.A.

WWW: http://evolution.genetics.washington.edu/phylip.html