Mesquite

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms.

Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed. Analyses include:

Reconstruction of ancestral states (parsimony, likelihood)
Tests of process of character evolution, including correlation
Analysis of speciation and extinction rates
Simulation of character evolution (categorical, DNA, continuous)
Parametric bootstrapping (integration with programs such as PAUP* and NONA)
Morphometrics (PCA, CVA, geometric morphometrics)
Coalescence (simulations, other calculations)
Tree comparisons and simulations (tree similarity, Markov speciation models)