ICHEC Software
Information about software packages installed on the ICHEC systems.
SWAPSC
Versions Installed
Stokes: 1.0b
Description
SWAPSC (Sliding Window Analysis Procedure for detecting Selective Constraints) is a computer software system 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. It 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
License
SWAPSC is freely available and distributed under the terms of the GNU Pubic License Agreement (Version 3).
Benchmarks
N/A.
Additional Notes
To use SWAPSC load the relevant environment module:
Further information can be obtained at http://bioinf.gen.tcd.ie/~faresm/page11/page11.html.
How to cite SWAPSC:
Fares M.A. (2004)
SWAPSC: sliding window analysis procedure to detect selective constraints.
Bioinformatics 20(16): 2867-2868.