[BiO BB] All-vs-All Global protein seq alignment score

[Goel, Manisha]

Hi All, 

I have a database of about 400 squences, which I want to compare
All-vs-All to get the global alignment score of each protein sequence
pair.
I tried using bl2seq but that gives me local alignments.
What other program would suit this function best ?
I would probably like to have the flexibility of being able to use
various matrices. 

Thanks a lot,
-Manisha


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