Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.
P4 is a Python package for maximum likelihood and Bayesian analysis of molecular sequences.
MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.