I just came across this algorithm for detecting recombination breakpoints, and it has got me wondering whether some of the sequences we flag as chimeric might simply include a recombination breakpoint. Thoughts, anyone?
Bioinformatics. 2006 Dec 15;22(24):3096-8. Epub 2006 Nov 16.
GARD: a genetic algorithm for recombination detection.
Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.