phylogenetic analysis of molecular sequence data using maximum-likelihood

 GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for
 inferring phylogenetic trees. Using an approach similar to a classical
 genetic algorithm, it rapidly searches the space of evolutionary trees
 and model parameters to find the solution maximizing the likelihood
 score. It implements nucleotide, amino acid and codon-based models of
 sequence evolution, and runs on all platforms. The latest version adds
 support for partitioned models and morphology-like datatypes.