[EMBOSS] Is there any way to use water or needle to do an all-to-all alignment?

[Jon Ison]

Hi Zhiqiang Ye

Have a look at the "allversusall" program in the EMBASSY "DOMALIGN" package:

http://emboss.sourceforge.net/apps/allversusall.html

It's beta software so go steady.  If it doesn't do exactly what you want
I'll gladly adapt it for you.  Let us know how you get on.

Cheers

Jon


> Hi, all
>    I want to do all-to-all pairwise comparison frequently. I have a
> fasta file "total.fasta" containing many sequences, I want to get the
> their pairwise comparison identities.  I don't want to split it to
> single fasta files and then needle them to the "total.fasta"  since I
> have to do this frequently.  Could needle or water be used for
> all-to-all alignment directly?  Just like blast.
>
>     Thank you very much.
>
> --
> Zhiqiang Ye
> PHD candidate
> College of Lifesciences, Center for Bioinformatics
> Peking University, Beijing.
>
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