BaTS

A Bayesian framework for measuring and testing phylogeny-trait associations

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Genie

A program for the inference of demographic history from molecular phylogenies

SHiAT

Generates plots of site-wise variation along a sequence alignment (including the Shannon Entropy and Hamming Distance measures)

BEAST

Bayesian Evolutionary Analysis Sampling Trees

Adapt-A-Rate

A program to estimate the rate of adaptive fixation in a population from sequences sampled at different points in time.

Hepatitis C Virus Subtyping Tool

An online program that uses phylogenetic methods to identify the subtype and genotype of query sequences.