Category: Phylogeny
Programs:
atv - Draw and edit 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)
mbiolegato - bioLegato interface for discrete state data (eg. molecular markers)
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
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
seqboot - Create resampled datasets
tbiolegato - bioLegato interface for phylogenetic trees
tGDE - GDE interface for phylogenetic trees
treedist - Calculate distance between trees
treetool - Phylogenetic tree editor
weighbor - weighted neighbor joining