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

Abstract

Summary: 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 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. Availability: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License. Contact: a.drummond@auckland.ac.nz; korbinian.strimmer@zoo.ox.ac.uk Supplementary information: An online description of the Application Programming Interface (API) of all public classes in PAL is available at http://www.pal-project.org/api/.