FastEpistasis is a high performance tool designed to test for epistasis effects when analysing continuous phenotypes. It computes tests of epistasis for a large number of SNP pairs, and is an efficient parallel extension to the PLINK epistasis module.
The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks.
RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package.