SWAPSC: sliding window analysis procedure to detect selective constraints
Fares, Mario A (2004) SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics, 20 (16). pp. 2867-2868.
Sliding-window analysis procedure to detect selective constraints (SWAPSC) is a software system to dissect the constraints on the evolution of protein-coding genes.The programestimates 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 nonsynonymous nucleotide substitutions. Thereafter, a statistical analysis is conducted to determine the optimum windowsize 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. A number of friendly useful output files is generated.
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