Recco (Recombination Analysis Using Cost Optimization) analyzes alignments of sequences that evolved subject to recombination and mutation. The analysis provides evidence as to whether a dataset contains recombination, which sequence is a recombinant and where the recombination breakpoints are. The analysis is based on explaining one sequence with all other sequences in the alignment using mutation and recombination. A parametric analysis of the parameter alpha, which weights recombination cost against mutation cost, yields additional information as to which sequence might be recombinant.
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:: MORE INFORMATION
Maydt, J. and T. Lengauer (2006).
“Recco: Recombination Analysis Using Cost Optimization.”,
Bioinformatics 2006, 22(9):1064-1071, doi:10.1093/bioinformatics/btl057.