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:




Documentation and 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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