Best/favorite global pairwise alignment program for proteins

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Khen

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Join Date: Mar 2012

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Best/favorite global pairwise alignment program for proteins

05-06-2013, 11:04 AM

I need a global pairwise alignment program that I can invoke from a Java and run on my local machine. My problem is that I have had garbage collection issues with biojava's alignment packages when I try to run many alignments at once, so I was wondering if anybody else had some ideas.
Any suggestions are appreciated!
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