[Biojava-l] Global Alignment

[Andreas Dräger]

Hello,

I just implemented the Needleman-Wunsch-Algorithm and an object for 
handling substitution matrices like BLOSSUM, PAM, GONNET and so on. It 
parses a matrix file and provides a method to get the costs for changing 
Symbol A to Symbol B. This is realized by two hashes and a private 
int[][] matrix.
If NeedlemanWunsch gets equal weights for gap opening and gap extension 
it won't consider affine gap penalties, whereas otherwise it will, which 
needs three times more memory.

Andreas Dräger
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