[Biojava-dev] Alignment algorithms

[Mark A Fortner]

I seem to recall that the neobio API already has both
the Smith-Waterman, and Needleman-Wunsch algorithms
implemented.  (http://neobio.sf.net)

As for ClustalW, I've seen several wrapper
implementations but no implementation in Java.

Hope this helps,

Mark Fortner
Mgr. Bioinformatics Software Dev
Lexicon Genetics


--- Rahul Karnik <rahul at genebrew.com> wrote:

> 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
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