Pebble (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) is a powerful application for Phylogenetic analysis. The primary purpose of Pebble is to provide tools for analysis and simulation of serially sampled sequence data (through maximum likelihood, and least-squares methods). Implemented forms of simulation include: trees, via a coalescent model, and sequence alignments, given an input tree and substitution model. Extra functionality includes data manipulation tools for sequence alignments and phylogenetic trees, as well as useful inbuilt alignment construction and editing facilities.
