[Biojava-dev] Pairwise similarity score speed

[Radhouane Aniba]

Hello Biojava people,

I have a question concerning Needlman Wunsh or Smith waterman algorithms.
I am using Biojava 1.7 and I read sequences from proteins fasta file then I
store my sequences into an array to calculate pairwise similarity scores
using a for loop.
The problem is that it is very time consuming if we want to calculate all
pairwise for a big number of protein sequences. I would like to know if
there is way to do a kind of "All against All" comparisons in one single
step ?
Do someone have a solution for this kind of problem ?

Thanks for help.

Radwen