[Biojava-dev] Java implementation of Smith-Waterman algorithm

[Ahmed Moustafa]

Hello,

I am working on a Java package of implementations of sequence alignment 
algorithms. I have released an implementation of Smith-Waterman 
algorithm with Gotoh's improvement. The time complexity is O(n2) and the 
space complexity is O(m * n + n) .

The package name is JAligner and it is hosted at sourceforge.net 
<http://jaligner.sourceforge.net>. There is a front-end demo using Swing 
and Java Web Start.

Could JAligner be incorporated into the BioJava project?

Best Regards,

Ahmed