|GARLI: Genetic Algorithm for Rapid Likelihood Inference|
GARLI uses a modified genetic algorithm to quickly infer phylogenies of nucleotide datasets. It uses the General Time Reversible (GTR) model of nucleotide substitution and simultaneously finds the mixture of topology, branch lengths, and rate heterogeneity and model parameters that maximizes the likelihood of the data fitting the phylogeny.
Using GARLI on HPC
GARLI requires non-interleaved input data in either PHYLIP or PAUP NEXUS format. It also requires a configuration file named "garli.conf" which can be seen here. Modify this configuration file to suit your needs, and then launch the serial version of GARLI with the command "garli." See the manual here, plus the Marine Biological Laboratory's Workshop on Molecular Evolution has a very good GARLI page.