The option to remove sequences using -seqoverlap and -resoverlap produces results I find unexpected. From what I can tell, it seems that when -resoverlap compares if a residue is the same in the other sequences it does not consider the base identity (for a DNA alignment), only whether there is a gap character or any DNA base. Therefore, for a gapfree alignment, if I change all bases in a sequence to e.g. "T" the sequence will not be removed from the alignment, even with strict settings, (e.g. -resoverlap 0.9 seqoverlap 95).

Is this how it is supposed to work and if so I'm curious why it works like this and not as I might have expected it to? Thanks