PHYLIP

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PHYLIP (PHYLogeny Inference Package) 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 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.[2] 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.[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 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.[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 a number of major phylogeny packages.

Phylip programs[edit]

The programs listed in PHYLIP are:[4]
Program Name Description
protpars Estimates phylogenies of protein 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. The distances can then be used in the distance matrix programs.
protdist Protein sequence distance method which computes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, Kimura's 1983 approximation to it, or a model based on the 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 produces 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 the 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 that an evolutionary clock is assumed.
neighbor An implementation of the Neighbor-Joining method and the UPGMA method.
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. This program can also do 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 take into account the correlations of characters.
contrast Reads a tree from a tree file, and a data set with continuous characters data, and produces 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 and 1). Allows use of the Wagner parsimony method, the Camin-Sokal parsimony method, or arbitrary mixtures of these.
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 and 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 and 1).
dolpenny Finds all 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 and 1) using the Dollo or polymorphism parsimony criteria. Evaluates parsimony and compatibility criteria for those phylogenies and 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 and 1). The largest clique (or all cliques within a given size range of the largest one) are found by a very fast branch and bound search method.
factor Character recoding program which takes discrete multistate data with character state trees and produces the corresponding data set with two states (0 and 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 unrooted phylogenies..
consense Consensus tree program which Computes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Is not able to compute the Adams consensus tree
treedist Computes the Robinson-Foulds symmetric difference distance between trees, which allows for differences in tree topology.
retree interactive tree rearrangement program which reads in a tree (with branch lengths if necessary) and allows you to reroot 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[edit]

  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.  edit
  2. ^ a b c "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. 

External links[edit]