[Biojava-dev] Support Pairwise Sequence Alignment based on BWT?

[Cai Shaojiang]

Dear BioJava developers:

I am a third-year Ph.D student from National University of Singapore. I am
doing some research on sequence alignment and genome assembly.

When looking at BioJava, I find that the it only supports basic pairwise
alignment algorithms like Smith-Waterman. Have you considered adding more
sophisticated ones like suffix tree, suffix array and FM-indexing based on
Burrows Wheeler Transform? I am actually very glad to contribute to the
implementations of them in Java. Thanks very much! Could anyone give some
advice?

Regards.

                        Carl.