i think i understand what you're after. a feature of the TK language is tagging in text/area fields. the tags are a way of marking positions (starting and ending) in text, which does not change the character count of the text. so what i have in mind is that you compare the reference sequence to each comparative sequence in turn, adding tags as you go. then at the end you do some post-processing to insert/delete/amend/other the text field depending on the tags inserted. or if you want the tags to immediately do something, you can bind them to actions (callbacks.) Anyway, I can't say enough about this really neat feature in TK. Most perls have TK or you can install it and the bindings.
hope that's what you were looking for.
the hardest line to type correctly is: stty erase ^H

In reply to Re: how to construct multiple sequence alignment from group of pairwise alignments by aquarium
in thread how to construct multiple sequence alignment from group of pairwise alignments by gudluck

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