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.^[1] The genetic data is analyzed for constraints in protein-coding sequence alignments.

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SWAPSC is used to dissect the constraints on the evolution of protein-coding genes.^[1] 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.^[1] 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.^[1]

The software system generates several user-friendly output files.^[1] SWAPSC has been implemented to run on either Microsoft Windows or Linux platforms.^[1]

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.^[1]

Notes

1. ^ ^{a b c d e f g} 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: BioInf-abstract-20-16-2867.

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: BioInf-abstract-20-16-2867.