I'm actually using OMA with this parameter:
- " # Type of input sequence data, has to be either 'DNA' or 'AA' InputDataType := 'DNA'; "
So OMA knows that I'm using DNA sequences. But I find this parameter inside the parameter file:
- " # alignments which have a score lower than MinScore will not be considered. # The scores are in Gonnet PAM matrices units. MinScore := 181; "
Gonnet PAM matrices being amino acid based, I would like to know if OMA convert DNA into AA before the allVSall step ?