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