PHYLIP

PHYLIP is a free Computational phylogenetics package of programs for inferring evolutionary trees (phylogenies). The name is an acronym for "PHYL"ogeny "I"nference "P"ackage. 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.cite web
url = http://evolution.genetics.washington.edu/phylip/general.html
accessdate = 2006-03-24
title = PHYLIP general information page] 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.cite book
authorlink= Joe Felsenstein
author = Joseph Felsenstein
url =http://www.sinauer.com/detail.php?id=1775#or(s)
publisher=Sinauer Associates
title=Inferring Phylogenies
date=August, 2003
id=ISBN 0-87893-177-5]

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 fragments, 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.

Phylip programs

Notes

External links

* [http://evolution.genetics.washington.edu/phylip/software.html Phylogeny Programs List] : A large list of phylogeny packages with details about each software. Current count at 263.

* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=7288891 Evolutionary trees from DNA sequences: a maximum likelihood approach.] : Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17:368–376.