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

[Zhiqiang Ye]

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.