Hi! I'm trying to do a pairwise alignment. As I explained in my previous post, I'm trying to filter the sequences by their alignment scores or end values. However, there is one thing that I can not understand in the results of alignments. There are gaps where mismatches should be and because of this, I am not able to filter the sequences by their length or score since it would be unreliable filtering.
Does anyone have any idea how can I solve this problem?
Thank you for your help!