SimPlot

Phylogenetic Analysis by Maximum Likelihood (PAML)

GENECONV Molecular Biology Computer Program

CAPS: coevolution analysis using protein sequences

PhyML

DAMBE

Cytoscape

CPHmodels 3.2 Server (protein structure)

InterMap3D

BEAST

BayesTraits

geiger: Analysis of evolutionary diversification

laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

ape: Analyses of Phylogenetics and Evolution