PHYLIP
PHYLogeny Inference Package is a free computational phylogenetics package of programs for inferring evolutionary trees. It consists of 35 portable programs, i.e., the source code is written in the programming language C. As of version 3.696, it is licensed as open-source software; versions 3.695 and older were proprietary software freeware. Releases occur as source code, and as precompiled executables for many operating systems including Windows, Mac OS 8, Mac OS 9, OS X, Linux ; and FreeBSD from FreeBSD.org.
Full documentation is written for all the programs in the package and is included therein. The author of the package is Professor Joseph Felsenstein, of the Department of Genome Sciences and the Department of Biology, University of Washington, Seattle.
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.
Each program is controlled through a menu, which asks users which options they want to set, and allows them to start the computation. The data is 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 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.
Output is written onto 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 seven major phylogeny packages.Component programs
