[Bioperl-l] Remove sites of an alignment

Tristan Lefebure tnl7 at cornell.edu
Wed Nov 28 10:44:17 EST 2007


Hello!

I was wondering if there was a function to remove sites/columns of an 
alignment. Something like: $aln->remove_sites(@sites_to_remove)
I looked around Bio::SimpleAlign but did not find exactly that. There is 
remove_columns, but it works on 'match'|'weak'|'strong'|'mismatch' criteria.

I could recycle the '_remove_col' sub-function of 'remove_columns' to do so 
(it splits the alignment into sequence objects, removes the sites, and then 
regenerates an alignment object), but I would be surprised if there was 
nothing already doing the job...

Thanks

-Tristan


More information about the Bioperl-l mailing list