category: Phylogeny

programs:

• blmarker - bioLegato interface for discrete state data (eg. molecular markers)
• bltree - bioLegato interface for phylogenetic trees
• clique - Compatability method for two-state characters
• confadd - Add confidence information (eg. bootstrap) to a phylogenetic tree
• 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
• fitch - Distance trees - Fitch/ Margoliash
• Gblocks - Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
• gendist - Compute genetic distances from gene frequencies
• kitsch - Distance trees - Fitch/ Margoliash (molecular clock)
• mesquite - A modular system for evolutionary analysis
• 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
• phylip.py - Classes used by Python scripts that run Phylip programs
• protdist - Construct distance matrix for protein sequences
• protpars - Protein parsimony
• restdist - Compute distance matrices for discrete data
• restml - Maximum likelihood phylogeny for discrete data
• retree - Rearrange and reroot phylogenetic trees
• seqboot - Create resampled datasets
• treedist - Calculate distance between trees
• weighbor - weighted neighbor joining