Hi!

Not a theoretical question, but not really a how-to either.

What does GARD do with missing data (end GAPS) and/or indels?

I have a dataset with a lot of long end-gaps (regions not sequenced) coded as gaps ('-'). Run as-is GARD quickly completed with no evidence of recombination. if I take those large-gap sequences out, GARD finds strong evidence for recombination.

Is it just stripping gap columns?

Thanks!

Darren