Keywords

meta-searching, phylogenetic analysis, scripting languages

Abstract

Due to the immensity of phylogenetic tree space for large data sets, researches must rely on heuristic searches to infer reasonable phylogenies. By designing meta-searches which appropriately combine a variety of heuristics and parameter settings, researchers can significantly improve the performance of heuristic searches. Advanced language constructs in the open-source PSODA project—including variables, mathematical and logical expressions, conditional statements, and user-defined commands—give researchers a better framework for the exploration and exploitation of phylogenetic meta-search algorithms. PSODA’s approach to scripting meta-search algorithms is unique among open-source packages and addresses several limitations of other phylogenetic applications.

Original Publication Citation

PsodaScript: Applying Advanced Language Constructs to Open-source Phylogenetic Search, J. L. Krein, A. R. Teichert, H. D. Carroll, M. J. Clement and Q. O. Snell, Proceedings of the 4th Biotechnology and Bioinformatics Symposium, October 27, pp 89-94.