Fares, Mario A.
SWAPSC: sliding window analysis procedure
to detect selective constraints.
Bioinformatics, 20 (16).
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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