After using screen.seqs my shortest sequence is 224 (NBases). Then applying filter.seqs(fasta=current, vertical=t, trump=.), all my sequences are shortened, with the shortest one now being 204 bp.

I’ve been wondering for quite a while now why this happens, but just accepted it. But if you only remove empty columns (i.e. only dots and dashes), why does this actually happen?
You’d at least expect that the shortest one doesn’t get any shorter, right?

Actually, trump=. will remove any column where a “.” appears in any sequence. So, if your 224 sequence extends outside of the alignment space you are targeting with the trump=., then those 20 bases will get cut.

Okay, that’s how I originally interpreted the manual, but somehow I lost my confidence.
Is there a way to eliminate the dots in front (alignment starts at 1044) and at the end beyond a certain value, say, your longest sequence?

Just doing vertical=T will get rid of most of the dots as well. You can also do pcr.seqs with start=1044 and end=whatever

Ok, thanks Herr Doctor :mrgreen: