Table 3.

List of tools and their description.

Tool name	Purpose
charnet	Computing clusters, trees and tripartitions in a network
cmpnets	Computing the distance between two networks
lca	Finding the last common ancestor of a set of nodes
mast	Computing the maximum agreement subtree
netpars	Scoring the parsimony of sequences on a pair of networks
riatahgt	Reconstructing HGT events from a pair of species/gene trees
rf	Computing the Robinson-Foulds tree measure

A table of the tools currently implemented in PhyloNet. With the exception of the three phylogenetic trees tools lca, mast, and rf, all the other tools are for analyzing reticulate evolutionary relationships.