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