PHYLIP 

PHYLIP (PHYLogeny Inference Package) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). It consists of 35 portable programs, i.e. the source code is written in C and precompiled executables are available for Windows (95/98/NT/2000/me/XP), Mac OS 8 and 9, Mac OS X, and Linux systems. Complete documentation is written for all the programs in the package and is part of the package. The author of this package is Joseph Felsenstein, Professor in the Department of Genome Sciences and the Department of Biology at the University of Washington, Seattle. Methods (implemented by each program) 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 fragment, distance matrices, and discrete characters. Each program is controlled through a menu, which asks the 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 (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. 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 a number of major phylogeny packages. (wikipedia)