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

[Peter Rice]

Hi Ye,

>    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.

It is possible to modify water to do this - read seqall and seqset as input, 
instead of sequenec and seqall, and process each sequence from the seqall 
against all sequences in the seqset.

It will be a new program (new input types). Not hard to do - you may want to 
try writing it.

It needs a new name. How about "waterfall" :-)

regards,

Peter