Garli

From BioPerl

Garli is a phylogenetic reconstruction program that performs "heuristic phylogenetic searches under the General Time Reversible (GTR) model of nucleotide substitution and its submodels, with or without gamma distributed rate heterogeneity and a proportion of invariant sites." It was written by Derrick Zwickl while a student in David Hillis's lab. It is available for download here.