An open source phylogenetic search and alignment package

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.

ChemAlign: Biologically Relevant Multiple Sequence Alignment Using Physicochemical Properties

“…ChemAlign is implemented in the software package PSODA [20]. PSODA is free and available for several operating systems at http://dna.cs.byu.edu/psoda.…”

Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

“…For this chapter I ignored POY, Garli, MEGA, RAxML, Phyml, and MrBayes as they are never or rarely used in morphology-based analyses. PSODA (Carroll et al 2007;Carroll et al 2009) seems to have only been cited 3 times according to GS and thus can also be safely discarded. That leaves just six terms and their variants to search for in the quest for morphologyphylogenies: PAUP*, Winclada, NONA, TNT, Hennig86, and PHYLIP.…”

Computer science and parsimony: a reappraisal, with discussion of methods for poorly structured datasets

“…Carroll et al. (, ) released a phylogeny package they call PSODA. They did not propose any new methods for tree searching, simply presenting a new implementation of stepwise addition of trees, branch‐swapping, and ratchet, which they compared only with Phylip and PAUP*.…”

“…The datasets used by Gregor et al (2013) were subsets of taxa from other datasets, and they cannot be reconstructed from their description of the experiments, so that their results cannot be checked directly. Carroll et al (2007Carroll et al ( , 2009) released a phylogeny package they call PSODA. They did not propose any new methods for tree searching, simply presenting a new implementation of stepwise addition of trees, branch-swapping, and ratchet, which they compared only with Phylip and PAUP*.…”