[Bioperl-l] issues with Bio::SimpleAlign add_seq function

albezg albezg at gmail.com
Thu Mar 19 17:30:35 EDT 2009

Hi all,
I'm using bioperl-1.6. Here are some things that bother me about
Bio::SimpleAlign add_seq function

1) Sequence order is counted from 0 not 1, unlike in other functions,
such as get_seq_by_pos and select.
2) If position $order is already occupied then the old sequence is
removed. Is there a way to insert a new sequence in the middle of an


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