PHYLIP, the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees).

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 executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp), MacOS X, MacOS 8 and 9, and Linux systems. Complete documentation is available on documentation files that come with the package. It includes programs to carry out parsimony, distance matrix methods, maximum likelihood, and other methods on a variety of types of data, including DNA and RNA sequences, protein sequences, restriction sites, 0/1 discrete characters data, gene frequencies, continuous characters and distance matrices. It is the most widely-distributed phylogeny package, with over 20,000 registered users, some of them satisfied.

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.

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 the ClustalW alignment program 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.

Here is the link to the package of Phylip : http://abies.nmsu.edu/pkgsrc/html/phylip/phylip.html. It contains Phylip programs and documentation.

The input for the phylogenetic programs in Phylip package is a file of sequences that have been previously aligned with a tool such as Clustal W and that is in the ‘Phylip format’. The input for the tree drawing programs will be the output from these files (please see flow chart) , many tools have pipelines set up to process the output of a given phylogeny tool such as dnaml to the next logical set of programs one may want to use.

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.

At this stage we do not have a mouse-windows interface for PHYLIP.

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 15,000 registered users.