PHYLIP

These programs include:

dnacomp
Estimates phylogenies from nucleic acid sequence data using the compatibility criterion.

dnadist
Computes four different distances between species from nucleic acid sequences.

dnainvar
For nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants.

dnaml
Estimates phylogenies from nucleotide sequences by maximum likelihood.

dnamlk
Same as DNAML but assumes a molecular clock.

dnamove
Interactive construction of phylogenies from nucleic acid sequences.

dnapars
Estimates phylogenies by the parsimony method using nucleic acid sequences.

dnapenny
Finds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search.

seqboot
Reads in a data set, and produces multiple data sets from it by bootstrap resampling.

consense
Computes consensus trees by the majority-rule consensus tree method.

protdist
Estimates phylogenies from protein sequences using the parsimony method.

protpars
Computes a distance measure for protein sequences.

restml
Estimation of phylogenies by maximum likelihood using restriction sites data.

fitch
Estimates phylogenies from distance matrix data under the "additive tree model" .

kitsch
Estimates phylogenies from distance matrix data under the "ultrametric" model.

neighbor
An implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method.

contml
Estimates phylogenies from gene frequency data by maximum likelihood under a model.

gendist
Computes one of three different genetic distance formulas from gene frequency data.

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.

mix
Estimates phylogenies by some parsimony methods for discrete character data with two states (0 and 1).

move
Interactive construction of phylogenies from discrete character data with two states (0 and 1).

penny
Finds all most parsimonious phylogenies for discrete-character data with two states.

dollop
Estimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states (0 and 1).

dolmove
Interactive construction of phylogenies from discrete character data with two states (0 and 1) using the Dollo or polymorphism parsimony criteria.

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.

clique
Finds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states.

factor
Takes discrete multistate data with character state trees and produces the corresponding data set with two states (0 and 1).

drawgram
Plots rooted phylogenies, cladograms, and phenograms in a wide variety of user-controllable formats.

drawtree
Similar to DRAWGRAM but plots unrooted phylogenies.

retree
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.