Phylip

The PHYLogeny Inference Package

Introduction

Phylip is a set of programs for inferring phylogenies and drawing trees. These programs are provided free by Joe Felsenstein and they run from the command line (see also the startup guide). As they may take a considerable amount of computer time, see the computer centre's rules on running compute-bound programs on the central servers. Versions of the programs are available for the PC and Mac (see the Phylip home page for details).

Phylip:

includes parsimony, distance matrix, and likelihood methods.
has programs for bootstrapping and generating consensus trees.
acts on molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.
parameters are entered through a menu list from which you select options to alter.
data files should be in plain text format.
uses "infile" as a default file name. It will ask for a file name if it can't be found.
writes output files to "outfile" or "treefile".
is run by entering the name of the program you wish to use (see below).

Documentation and Programs

Brief description of the programs.
Overview of Phylip.
Sequence formats and programs.
Distance matrix programs.
Continuous character and gene frequency programs.
Discrete character programs.
Tree drawing programs.

The programs:

---------- Programs for molecular sequence data ----------

protpars Protein parsimony dnapars Parsimony method for DNA

dnamove Interactive DNA parsimony dnapenny Branch and bound for DNA

dnacomp Compatibility for DNA dnainvar Phylogenetic invariants

dnaml Maximum likelihood method dnamlk DNA ML with molecular clock

dnadist Distances from sequences protdist Distances from proteins

restml ML for restriction sites seqboot Bootstraps sequence data sets

----------- Programs for distance matrix data ------------

fitch Fitch-Margoliash and least-squares methods kitsch Fitch-Margoliash and least squares methods with evolutionary clock

neighbor Neighbor-joining and UPGMA methods

-------- Programs for gene frequencies and continuous characters -------

contml Maximum likelihood method gendist Computes genetic distances

contrast Computes contrasts and correlations for comparative method studies

------------- Programs for 0-1 discrete state data -----------

mix Wagner, Camin-Sokal, and mixed parsimony criteria move Interactive Wagner, C-S, mixed parsimony program

penny Finds all most parsimonious trees by branch-and-bound dollop same as preceding programs, but for the Dollo parsimony criteria

dolmove same as preceding programs, but for the Dollo parsimony criteria dolpenny same as preceding programs, but for the polymorphism parsimony criteria

clique Compatibility method factor recode multistate characters

---------- Programs for plotting trees and consensus trees -------

drawgram Draws cladograms and phenograms on screens, plotters and printers drawtree Draws unrooted phylogenies on screens, plotters and printers

consense Majority-rule and strict consensus trees retree Reroots, changes names and branch lengths, and flips trees

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---------- Programs for molecular sequence data ----------
protpars	Protein parsimony	dnapars	Parsimony method for DNA
dnamove	Interactive DNA parsimony	dnapenny	Branch and bound for DNA
dnacomp	Compatibility for DNA	dnainvar	Phylogenetic invariants
dnaml	Maximum likelihood method	dnamlk	DNA ML with molecular clock
dnadist	Distances from sequences	protdist	Distances from proteins
restml	ML for restriction sites	seqboot	Bootstraps sequence data sets
----------- Programs for distance matrix data ------------
fitch	Fitch-Margoliash and least-squares methods	kitsch	Fitch-Margoliash and least squares methods with evolutionary clock
neighbor	Neighbor-joining and UPGMA methods
-------- Programs for gene frequencies and continuous characters -------
contml	Maximum likelihood method	gendist	Computes genetic distances
contrast	Computes contrasts and correlations for comparative method studies
------------- Programs for 0-1 discrete state data -----------
mix	Wagner, Camin-Sokal, and mixed parsimony criteria	move	Interactive Wagner, C-S, mixed parsimony program
penny	Finds all most parsimonious trees by branch-and-bound	dollop	same as preceding programs, but for the Dollo parsimony criteria
dolmove	same as preceding programs, but for the Dollo parsimony criteria	dolpenny	same as preceding programs, but for the polymorphism parsimony criteria
clique	Compatibility method	factor	recode multistate characters
---------- Programs for plotting trees and consensus trees -------
drawgram	Draws cladograms and phenograms on screens, plotters and printers	drawtree	Draws unrooted phylogenies on screens, plotters and printers
consense	Majority-rule and strict consensus trees	retree	Reroots, changes names and branch lengths, and flips trees