vanilla - phylogeny tools
linux-intel, solaris-amd64, solaris-sparc
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).