Keywords

sequence analysis, PSODA, open source

Abstract

PSODA is an open source (GPL v2) sequence analysis package that implements sequence alignment using biochemical properties, phylogeny search with parsimony or maximum likelihood criteria and selection detection using biochemical properties (TreeSAAP ). PSODA is compatible with PAUP and the search algorithms are competitive with those in PAUP. PSODA also adds a basic scripting language to the PAUP block, making it possible to easily create advanced meta-searches. Because PSODA is open-source, we have also been able to easily add in advanced search techniques and characterize the benefits of various optimizations. PSODA is available for Macintosh OS X, Windows, and Linux.

Original Publication Citation

PSODA: Open Source Phylogenetic Search and DNA Analysis, Quinn Snell, Mark Clement, Kenneth Sundberg, Proceedings of the Bioinformatics Open Source Conference (BOSC) 29, Stockholm Sweden.