PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). It is available free over the Internet, and written to work on as many different kinds of computer systems as possible. The source code is distributed (in C), and for some particular systems executables are also distributed. In particular, already-compiled executables are available for Windows95/98/NT, Windows 3.x, DOS, PowerMac, and 68k Macintosh 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, 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.

At this stage we do not have a mouse-windows interface for PHYLIP, except that it is possible to click on the lines of the menu in the Macintosh and PowerMac executable versions.

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.

... to the PHYLIP home page