JCoDA: a tool for detecting evolutionary selection

Background: The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. Results: JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Infe...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Steven N. Steinway, Ruth Dannenfelser, Christopher D. Laucius, James E. Hayes, Sudhir Nayak
• Keywords: BMCBI 2010, Coding Sequences, Evolutionary Selection, Sex Determination Pathway