Title: An open source phylogenetic search and alignment package

Authors: Hyrum Carroll, Adam R. Teichert, Jonathan Krein, Kenneth Sundberg, Quinn Snell, Mark Clement

Addresses: Computer Science Department, Brigham Young University, Provo, Utah 84602, USA. ' Computer Science Department, Brigham Young University, Provo, Utah 84602, USA. ' Computer Science Department, Brigham Young University, Provo, Utah 84602, USA. ' Computer Science Department, Brigham Young University, Provo, Utah 84602, USA. ' Computer Science Department, Brigham Young University, Provo, Utah 84602, USA. ' Computer Science Department, Brigham Young University, Provo, Utah 84602, USA

Abstract: PSODA is a comprehensive phylogenetics package, including alignment, phylogenetic search under both parsimony and maximum likelihood, and visualisation and analysis tools. PSODA offers performance comparable to PAUP^* in an open source package that aims to provide a foundation for researchers examining new phylogenetic algorithms. A key new feature is PsodaScript, an extension to the nearly ubiquitous NEXUS format, that includes conditional and loop constructs; thereby allowing complex meta-search techniques like the parsimony ratchet to be easily and compactly implemented. PSODA promises to be a valuable tool in the future development of novel phylogenetic techniques. This paper seeks to familiarise researchers with PSODA and its features, in particular the internal scripting language, PsodaScript. PSODA is freely available from the PSODA.

Keywords: PSODA; PsodaScript; phylogenetic inference; open source; bioinformatics; phylogenetic search; phylogenetic alignment; visualisation.

DOI: 10.1504/IJBRA.2009.026424

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.3, pp.349 - 364

Published online: 11 Jun 2009 *

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