PAL: An object-oriented programming library for molecular evolution and phylogenetics

Abstract

Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27 000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers.