It's not clear to me what you are actually asking for help with here?

Do you already know where the insertion points are and just need help with adding the dashes in the right places?

Or are you looking for an algorithm that allows you to find the insertion points?

Also, little data and/or a worked example goes a long. If you have a set of sequences--shorted to say 200/300 chars; don't post megabytes sequences) that demonstrate what you need to do, it is usually much clearer to non-bio(*) monks.

(*)Good'ol fashioned soap was good enough for my mum...{drone}... :)

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
RIP an inspiration; A true Folk's Guy

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

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