Software

BaTS

A Bayesian framework for measuring and testing phylogeny-trait associations

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.

Seraphim

An R package that combines GIS and phylogeographic methods to test whether environmental factors can explain ecological dispersal.

ClusterByTime

A Java program that can extract clusters defined by a threshold TMRCA from molecular clock phylogenies.

Perspectev

An R package that analyses the extent to which differential survival with respect to higher level trait variation is reducible to lower level variation.