PHYLIP

PHYLogeny Inference Package
Original author(s) Joseph Felsenstein
Developer(s) University of Washington
Initial release October 1980 (1980-10)
Stable release
3.696 / 2 November 2014 (2014-11-02)
Development status Active
Written in C
Operating system Windows, Mac OS X, Linux
Platform x86, x86-64
Available in English
Type Phylogenetics
License => v3.696: open-source
=< v3.695: proprietary freeware
Website evolution.genetics.washington.edu/phylip.html

PHYLogeny Inference Package (PHYLIP) is a free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).[1] 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 (95, 98, ME, NT, 2000, XP, Vista), Mac OS 8, Mac OS 9, OS X, Linux (Debian, Red Hat); and FreeBSD from FreeBSD.org.[2] 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.[3]

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.[2]

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 (but this text file cannot be in the special format of that word processor, it must 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.[2]

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

Programs listed in PHYLIP[4]
Program name Description
protpars Estimates phylogenies of peptide sequences using the parsimony method
dnapars Estimates phylogenies of DNA sequences using the parsimony method
dnapenny DNA parsimony branch and bound method, finds all of the most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search
dnamove Interactive construction of phylogenies from nucleic acid sequences, with their evaluation by DNA parsimony method, with compatibility and display of reconstructed ancestral bases
dnacomp Estimates phylogenies from nucleic acid sequence data using the compatibility criterion
dnaml Estimates phylogenies from nucleotide sequences using the maximum likelihood method
dnamlk DNA maximum likelihood method with molecular clock; using both dnaml and dnamlk together permits a likelihood-ratio test for the molecular clock hypothesis
proml Estimates phylogenies from protein amino acid sequences by using the maximum likelihood method
promlk Protein sequence maximum likelihood method with molecular clock
restml Estimation of phylogenies by maximum likelihood using restriction sites data; not from restriction fragments but from the presence or absence of individual sites
dnainvar For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants, which test alternative tree topologies
dnadist DNA distance method which computes four different distances between species from nucleic acid sequences; distances can then be used in the distance matrix programs
protdist Protein sequence distance method which computes a distance measure for sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, Kimura's 1983 approximation to it, or a model based on genetic code plus a constraint on changing to a different category of amino acid
restdist Distances calculated from restriction sites data or restriction fragments data
seqboot Bootstrapping-jackknifing program; reads in a data set, and emits multiple data sets from it by bootstrap resampling
fitch Fitch-Margoliash distance matrix method; estimates phylogenies from distance matrix data under the additive tree model according to which the distances are expected to equal the sums of branch lengths between species
kitsch Fitch-Margoliash distance matrix method with molecular clock; estimates phylogenies from distance matrix data under the ultrametric model which is the same as the additive tree model except an evolutionary clock is assumed
neighbor Implementation of the methods neighbor joining and UPGMA
contml Maximum likelihood continuous characters and gene frequencies; estimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is due to genetic drift in the absence of new mutations; also does maximum likelihood analysis of continuous characters that evolve by a Brownian Motion model, assuming that the characters evolve at equal rates and in an uncorrelated fashion; does not account for character correlations
contrast Reads a tree from a tree file, and a data set with continuous characters data, and emits the independent contrasts for those characters, for use in any multivariate statistics package
gendist Genetic distance program which computes one of three different genetic distance formulas from gene frequency data
pars Unordered multistate discrete-characters parsimony method
mix Estimates phylogenies by some parsimony methods for discrete character data with two states (0, 1); allows using methods: Wagner, Camin-Sokal, or arbitrary mixes
penny Branch and bound mixed method which finds all of the most parsimonious phylogenies for discrete-character data with two states, for the Wagner, Camin-Sokal, and mixed parsimony criteria using the branch-and-bound method of exact search
move Interactive construction of phylogenies from discrete character data with two states (0, 1); evaluates parsimony and compatibility criteria for those phylogenies and displays reconstructed states throughout the tree
dollop Estimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states (0, 1)
dolpenny Finds all or most parsimonious phylogenies for discrete-character data with two states, for the Dollo or polymorphism parsimony criteria using the branch-and-bound method of exact search
dolmove Interactive construction of phylogenies from discrete character data with two states (0, 1) using the Dollo or polymorphism parsimony criteria; evaluates parsimony and compatibility criteria for those phylogenies; displays reconstructed states throughout the tree
clique Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states (0, 1); the largest clique (or all cliques within a given size range of the largest one) are found by a fast branch and bound search method
factor Character recoding program which takes discrete multistate data with character state trees and emits the corresponding data set with two states (0, 1)
drawgram Rooted tree drawing program which plots rooted phylogenies, cladograms, and phenograms in a wide variety of user-controllable formats. The program is interactive and allows previewing of the tree on PC or Macintosh graphics screens, and Tektronix or Digital graphics terminals.
drawtree Unrooted tree drawing program similar to DRAWGRAM, but plots phylogenies
consense Consensus tree program which computes trees by the majority-rule tree method, which also allows easily finding the strict consensus tree; unable to compute Adams consensus tree
treedist Computes the Robinson–Foulds symmetric difference distance between trees, which allows differences in tree topology
retree Interactive tree rearrangement program which reads in a tree (with branch lengths if needed) and allows rerooting the tree, to flip branches, to change species names and branch lengths, and then write the result out; can be used to convert between rooted and unrooted trees

References

  1. ↑ Felsenstein, J. (1981). "Evolutionary trees from DNA sequences: A maximum likelihood approach". Journal of Molecular Evolution. 17 (6): 368–376. doi:10.1007/BF01734359. PMID 7288891.
  2. 1 2 3 "PHYLIP general information page". Retrieved 2010-02-14.
  3. ↑ Joseph Felsenstein (August 2003). Inferring Phylogenies. Sinauer Associates. ISBN 0-87893-177-5.
  4. ↑ "PHYLIP package documentation mirror site". Retrieved 2006-03-24.
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