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
• flat2phyl - Convert a GDE flatfile into a Phylip discrete character file
• 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
• 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
• retree - Rearrange and reroot phylogenetic trees
• seqboot - Create resampled datasets
• tGDE - GDE interface for phylogenetic trees
• treedist - Calculate distance between trees
• 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