[Seqan-dev] Realigning over Amino Acids

[Gregory Burgess <gburgess@hawaii.edu>]

Hi,

I'm using seqan 1.4.1.  I have a fasta file of aligned (gap characters included) amino acid sequences.  I would like to simply read in this file and use seqan's realign function over these sequences. 

I see that realign() requires a Fragment Store, but I'm not sure how to generate the appropriate data structures from already-aligned amino acid sequences.  Can someone provide a general outline of this (or another approach)?

Thanks,

Greg