- atv - Draw and edit phylogenetic trees
- blmarker - bioLegato interface for discrete state data (eg. molecular markers)
- bltree - bioLegato interface for phylogenetic trees
- clique - Compatability method for two-state characters
- consense - Consensus trees
- contml - Gene Frequencies and Continuous Characters Maximum Likelihood
- contrast - compute contrasts for comparative method
- dnacomp - DNA phylogeny using compatability method
- dnadist - Construct distance matrix for DNA sequences
- dnainvar - DNA sequence phylogeny invariants
- dnaml - DNA phylogeny using Maximum Likelihood
- dnamlk - DNA phylogeny using Maximum Likelihood (with evolutionary clock)
- dnamove - DNA parsimony with interactive tree rearrangement
- dnapars - DNA parsimony
- dnapenny - DNA parsimony using branch and bound method
- dollop - Discrete data parsimony method of DOLLO
- dolmove - Interactive Dollo and Polymorphism Parsimony
- dolpenny - Branch and bound parsimony using Dollo and polymorphism methods
- drawgram - Draw cladograms
- drawtree - Draw radial trees
- factor - Generate discrete (0,1) characters from multistate characters
- fastDNAml - DNA maximum likelihood
- fitch - Distance trees - Fitch/ Margoliash
- flat2phyl - Convert a GDE flatfile into a Phylip discrete character file
- gendist - Compute genetic distances from gene frequencies
- kitsch - Distance trees - Fitch/ Margoliash (molecular clock)
- mesquite - A modular system for evolutionary analysis
- mGDE - GDE interface for discrete state data (eg. molecular markers)
- mix - Mixed method discrete character parsimony
- move - Interactive mixed-method parsimony
- mrbayes - Bayesian inference of phylogeny
- neighbor - Distance trees - Neighbor-Joining/UPGMA
- pars - Discrete character parsimony
- penny - Branch and bound parsimony for discrete data
- phyl2flat - Convert a Phylip discrete character file into a GDE flatfile
- phylip.py - Classes used by Python scripts that run Phylip programs
- phylo_win - Phylogenetic analysis workbench
- protdist - Construct distance matrix for protein sequences
- protpars - Protein parsimony
- restdist - Compute distance matrices for discrete data
- restml - Maximum likelihood phylogeny for discrete data
- reticulate - Detect reticulate evolution by DNA compatability
- retree - Rearrange and reroot phylogenetic trees
- seqboot - Create resampled datasets
- tGDE - GDE interface for phylogenetic trees
- treedist - Calculate distance between trees
- treetool - Phylogenetic tree editor
- v_concat - Concatenates a set of sequence alignments.
- v_demograph - Estimates demographic parameters (effective population size, growth rate) by maximizing the coalescent prior for a single given clocklike tree.
- v_disttree - Tree methods dealing with distance matrices.
- v_evolve - Generates artificial data sets for a tree and a model of sequence evolution (available models are the same as in MLTREE and MLDIST)
- v_mldist - Computes pairwise maximum-likelihood distance matrices for nucleotide, amino acid, and two-state data under a variety of substitution models
- v_mltree - Computes likelihoods of trees under a variety of substitution models (see MLDIST)
- v_reroot - Reads a treefile (NH format) and reroots the tree, making node the new root.
- v_rewrite - Reads a data set and reformats it into various formats
- v_showtree - Reads treefile (NH format), generates ASCII picture, and computes distance matrix induced by branch length.
- v_splitcodon - Separate 1st, 2nd, 3rd codon positions of an alignment into separate file.
- v_treecomp - Reads two trees, each from a different file, and computes the Robinson Foulds score (topological distance measure based on splits).
- weighbor - weighted neighbor joining