Relaxed phylogenetics and dating with confidence drummond
The BEAST software package is an ambitious attempt to provide a general framework for parameter estimation and hypothesis testing of evolutionary models from molecular sequence data.
BEAST is a Bayesian statistical framework and thus provides a role for prior knowledge in combination with the information provided by the data.
Firstly, Bayesian methods allow the relatively straightforward implementation of extremely complex evolutionary models.
Secondly, there is an often erroneous perception that Bayesian estimation is "faster" than heuristic optimization based on a maximum likelihood criterion.
The purpose behind the development of BEAST is to bring a large number of complementary evolutionary models (substitution models, insertion-deletion models, demographic models, tree shape priors, relaxed clock models, node calibration models) into a single coherent framework for evolutionary inference.
BEAST source code is object-oriented, modular in design and freely available at BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation.The motivation for doing this is (1) to avoid the unnecessary simplifying assumptions that currently exist in many evolutionary analysis packages and (2) to provide new model combinations and a flexible system for model specification so that researchers can tailor their evolutionary analyses to their specific set of questions.The ambition of this project requires teamwork, and we hope that by making the source code of BEAST freely available, the range of models implemented, while already large, will continue to grow and diversify.This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics.Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree.