[Bioperl-l] again on remove gapped columns

[luisa pugliese]

Hi,
many thanks to everybody who reply to my message. I tryed your suggestions
and I found the both:
$aln->remove_gaps and $aln->remove_columns(['gaps']), remove all the columns
where in one sequence there is a gap and if in the other sequence there are
no gaps, the aa or nucleotides are removed. This changes the alignment and
of course it is not what I want. Does anybody have any other suggestion
other than reading the alignment files with another program and writing them
out (I already tryed this with AlignIO and it doesn't work)?
Best regards
Luisa
=============================
Luisa Pugliese, Ph.D.
luisa.pugliese at safan-bioinformatics.it
S.A.F.AN. BIOINFORMATICS
Corso Tazzoli 215/13 -10137 Torino
tel +39 011 3026230
cell. +39 333 6130644