PHYLIP is a free computational phylogenetics

Computational phylogenetics

Computational phylogenetics is the application of computational algorithms, methods and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa...

 package of programs for inferring evolutionary trees (phylogenies

Phylogenetics

In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...

). The name is an acronym for PHYLogeny Inference Package. It consists of 35 portable

Porting

In computer science, porting is the process of adapting software so that an executable program can be created for a computing environment that is different from the one for which it was originally designed...

 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

Joe Felsenstein

Joseph "Joe" Felsenstein is Professor in the Departments of Genome Sciences and Biology and Adjunct Professor in the Departments of Computer Science and Statistics at the University of Washington in Seattle...

, 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

Distance matrix

In mathematics, computer science and graph theory, a distance matrix is a matrix containing the distances, taken pairwise, of a set of points...

, and likelihood method

Maximum likelihood

In statistics, maximum-likelihood estimation is a method of estimating the parameters of a statistical model. When applied to a data set and given a statistical model, maximum-likelihood estimation provides estimates for the model's parameters....

s, 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

Newick format

In mathematics, Newick tree format is a way to represent graph-theoretical trees with edge lengths using parentheses and commas. It was adopted by James Archie, William H. E. Day, Joseph Felsenstein, Wayne Maddison, Christopher Meacham, F...

, an informal standard agreed to in 1986 by authors of a number of major phylogeny packages.

Phylip programs

The programs listed in PHYLIP are:

Program Name	Description
protpars	Estimates phylogenies of protein sequences using the Parsimony Maximum parsimony Parsimony is a non-parametric statistical method commonly used in computational phylogenetics for estimating phylogenies. Under parsimony, the preferred phylogenetic tree is the tree that requires the least evolutionary change to explain some observed data....  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 Maximum likelihood In statistics, maximum-likelihood estimation is a method of estimating the parameters of a statistical model. When applied to a data set and given a statistical model, maximum-likelihood estimation provides estimates for the model's parameters....  method.
dnamlk	DNA maximum likelihood method with molecular clock. Using both dnaml and dnamlk together permits a likelihood-ratio test Likelihood-ratio test In statistics, a likelihood ratio test is a statistical test used to compare the fit of two models, one of which is a special case of the other . The test is based on the likelihood ratio, which expresses how many times more likely the data are under one model than the other...  for the molecular clock Molecular clock The molecular clock is a technique in molecular evolution that uses fossil constraints and rates of molecular change to deduce the time in geologic history when two species or other taxa diverged. It is used to estimate the time of occurrence of events called speciation or radiation...  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 Point accepted mutation Point accepted mutation , is a set of matrices used to score sequence alignments. The PAM matrices were introduced by Margaret Dayhoff in 1978 based on 1572 observed mutations in 71 families of closely related proteins... , 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 Data set A data set is a collection of data, usually presented in tabular form. Each column represents a particular variable. Each row corresponds to a given member of the data set in question. Its values for each of the variables, such as height and weight of an object or values of random numbers. Each... , and produces multiple data sets from it by bootstrap resampling.
fitch	Fitch-Margoliash distance matrix Distance matrix In mathematics, computer science and graph theory, a distance matrix is a matrix containing the distances, taken pairwise, of a set of points...  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 Neighbor-joining In bioinformatics, neighbor joining is a bottom-up clustering method for the creation of phenetic trees , created by Naruya Saitou and Masatoshi Nei...  method and the UPGMA UPGMA UPGMA is a simple agglomerative or hierarchical clustering method used in bioinformatics for the creation of phenetic trees...  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 Robinson-Foulds metric The Robinson–Foulds metric is a way to measure the distance between unrooted phylogenetic trees. It is defined as where A is the number of partitions of data implied by the first tree but not the second tree and B is the number of partitions of data implied by the second tree but not the first... 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.

External links

• Phylogeny Programs List: A large list of phylogeny packages with details about each software. at 366.