Package: vanilla

vanilla - phylogeny tools
Documentation
	$local/doc/vanilla/index.html
	$local/doc/vanilla/license.html
Data
Platforms: linux-intel, solaris-amd64, solaris-sparc
Installation: local
Programs:
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).