[Biojava-dev] Alignment algorithms

[Rahul Karnik]

While reading through "Biological Sequence Analysis", I am finding it 
useful to reimplement some standard alignment algorithms in Java. 
Looking through the current Biojava package, I see that alignment is 
limited to HMM based methods. Would there be any interest in patches 
that add some standard alignment algorithms to the Biojava package? The 
ones I had in mind were Smith-Waterman (with substitution matrices), 
ClustalW and TCoffee. Along those lines, what would the appropriate 
package to use for such classes? And where should the substitution 
matrices go?

Thanks,
Rahul