SWAPSC is the software of the Sliding Window Analysis Procedure to detect Selective Constraints in protein-coding genes. The program estimates rates of nucleotide substitutions at specific codon regions in each branch of a phylogenetic tree. The program uses several sets of simulated sequence alignments to estimate the probability of synonymous and non-synonymous nucleotide substitutions. Thereafter, a statistical analysis is conducted to determine the optimum window size to detect selective constraints. Finally, the optimum window size is slid along the real alignment and a test for significance of the estimated number of synonymous and non-synonymous nucleotide substitutions in each sliding step is conducted.
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Bioinformatics. 2004 Nov 1;20(16):2867-8. Epub 2004 May 6.
SWAPSC: sliding window analysis procedure to detect selective constraints.