PHYLIP (acronym for PHYLogeny Inference Package) is a free package of programs for inferring phylogenies (evolutionary trees). PHYLIP is written to work on as many different kinds of computer systems as possible.
In particular, already-compiled executables are available for Mac OS X, Windows (95/98/NT/2000/me/xp/Vista), and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. Complete documentation is available on documentation files that come with the package.
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 and fragments, distance matrices, and discrete characters.
Output is written onto special files with names like "outfile" and "outtree". Trees written onto "outtree" are in the Newick format, an informal standard agreed to in 1986 by authors of a number of major phylogeny packages.
