title: JCoDA: a tool for detecting evolutionary selection.
abstract: 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 Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway.
  
  
  CONCLUSIONS
  JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda.
authors.affiliation: Department of Biology, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA.
authors.forename: Steven N
authors.initials: SN
authors.lastname: Steinway
authors.forename: Ruth
authors.initials: R
authors.lastname: Dannenfelser
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Laucius
authors.forename: James E
authors.initials: JE
authors.lastname: Hayes
authors.forename: Sudhir
authors.initials: S
authors.lastname: Nayak
mesh_terms: D003062:Codon / Q000235:genetics; D030541:Databases, Genetic; D030562:Databases, Protein; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods*; D016415:Sequence Alignment; D012984:Software
chemical_list: D003062:Codon