Construct Multiple Sequence Alignment From Pairwise Alignment.

Question

[User 0431]

I would like to construct the multiple sequence alignment from the pairwise one. do one have any nice source code that do this..

[Lars Juhl Jensen]

I think you misunderstand the purpose of flagging messages as requiring moderator attention. So far you have tagged both of your own questions. It is not meant to try to get our attention to your your questions. It is meant to point out to us if there are serious problems with content posted by others.

[Chris Miller]

You're going to have to be more specific about what you're trying to accomplish if you hope to receive help. Please edit your question to add more details, otherwise, it's likely to be deleted.

[User 0431]

I m sorry for that tag..I misunderstand the function to used it.

Answer 1

[Andreas]

Hi,

Cedric Notredame's T-Coffee can do that. In fact that's how it works: it builds pairwise alignments of all possible pairs (you can also use only a few or many alternative ones) and turns them into a so-called library. That gets checked for consistency, extended through triplet comparisons etc. and from there a multiple alignment is build.

The procedure to use your own pairwise alignments as input should be described in the T-Coffee manual

Andreas

[User 0431]

thank you so much for your answer..it is really what I m looking for...I have read the t-coffee but it seems more complicated to understand the source code.. could you please if you can explain in more details. How can I write a code similar to what have been done in t-coffee?

[Andreas]

You don't have to write any code. T-Coffee has the capability to use your pairwise alignments as such. You just have to use the correct commandline. See section "Q: I want to build my own libraries." on http://www.tcoffee.org/Documentation/t_coffee/t_coffee_tutorial.htm