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

[Zhang Chen]

I think what you want is not difficult to implement with the help of Bioperl.
A little work on scripts and Bio::Factory::EMBOSS may help you.

2005/11/18, Zhiqiang Ye <yezhiqiang at gmail.com>:
> 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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