An open source phylogenetic search and alignment package

Authors:
Hyrum Carroll;Adam R. Teichert;Jonathan Krein;Kenneth Sundberg;Quinn Snell;Mark Clement
Affiliations:
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
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2009

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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.