Swapsc

The SWAPSC package, or Sliding Window Analysis Procedure for detecting Selective Constraints, is a computer software system, published in May 2004, for analyzing genetic data structured for a biological family tree, or phylogenetic tree. Mario A. Fares, Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland, "Bioinformatics", vol. 20 issue 16, Oxford University Press, May 2004, pp. 2867-2868, webpage: [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/16/2867 BioInf-abstract-20-16-2867] .] The genetic data is analyzed for constraints in protein-coding sequence alignments.

SWAPSC is used to dissect the constraints on the evolution of protein-coding genes. The software estimates rates of the nucleotide substitutions along specific codon regions within each branch of a phylogenetic tree. The program uses many sets of simulated sequence alignments when estimating the probabilities of synonymous and non-synonymous nucleotide substitutions. Afterward, the software conducts a statistical analysis to determine the optimum window size for detecting selective constraints. Finally, the optimum window size is slid along the real alignment, and a test is conducted to rate significance of the estimated number of synonymous and non-synonymous nucleotide substitutions within each sliding step.

The software system generates several user-friendly output files. SWAPSC has been implemented to run on either Microsoft Windows or Linux platforms.

Availability: SWAPSC is available at:: http://www.may.ie/academic/biology/staff/mfmolecevolandbioinf.shtml Distribution versions for both Linux & MS Windows systems are available, including a manual and example files.

Notes

References

* Mario A. Fares, Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland, "Bioinformatics", vol. 20 issue 16, Oxford University Press, May 2004, pp. 2867-68, webpage: [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/16/2867 BioInf-abstract-20-16-2867] .