[Bioperl-l] mega next_aln unmatch

Nathan Haigh nathanhaigh at ukonline.co.uk
Fri Aug 13 07:27:31 EDT 2004

I've been playing with some of the alignment file formats and I've noticed
that when a mega file is read in it returns an alignment object that
contains the the sequences as represented in the mega file (i.e. with dots
for matched chars etc).

I'm not sure how all the other alignment format objects return their
sequences, but wouldn't it make more sense to return the object with the
chars converted back to sequence chars? i.e. make a call to $aln->unmatch()
prior to returning the alignment object at the end of mega.pm? I've just
seen that nexus.pm also makes the same call, so mega.pm should probably also
be brought into line with this also.


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