HYPHY

HYPHY is an open-source software package for comparative sequence analysis using stochastic evolutionary models. It provides a suite of advanced phylogenetic methods to detect and test for natural selection, recombination, co-evolution, and rate variation across genes and lineages. HYPHY implements state-of-the-art statistical models to answer fundamental evolutionary questions, including the detection of episodic and pervasive selection, as well as recombination events.