I would like to construct the multiple sequence alignment from the pairwise one. do one have any nice source code that do this..
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User 0431 •
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
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?
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
MAFFT offers various multiple alignment strategies. They are classified into three types, (a) the progressive method, (b) the iterative refinement method with the WSP score, and (c) the iterative refinment method using both the WSP and consistency scores. In general, there is a tradeoff between speed and accuracy. The order of speed is a > b > c, whereas the order of accuracy is a [?]viagra without prescriptions[?]. The results of benchmarks can be seen here. The following are the detailed procedures for the major options of MAFFT.
This comment puzzles me - the first half is quite informative and then it goes downhill, starting from viagra with a nonsense link. Then the following two sentences point to some materials but with no links. Would you consider editing this comment, so that this can be helpful? Thanks.
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I m sorry for that tag..I misunderstand the function to used it.