[Biojava-l] Alignmente algorithms implemented by BioJava

[Sylvain Foisy]

Hi there,

The CVS code in BioJava contains the necessary classes to perform both
Smith-Waterman and Needleman-Wunch pairwise alignments. Just have a look at
the Javadocs for instructions. The preferred way around here is based around
using HMMs to perform the alignments; for this look at the Cookbook section
of the BioJava's new website for ways to do that
(http://biojava.open-bio.org).

As far as MSA are concerned, I don't think that there is anything to do that
in BJ. You could call clustal from within your program and use BJ's MSA
parsing classes to do your stuff.

Hope this helps

Sylvain


On 3/9/06 11:59 AM, "[NAME]" <[ADDRESS]> wrote:

> Hi,
>  
> Can somebody tell me what algorithms Biojava uses to make local alignments and
> multiples alignments?
> I'm Serching it on the Documentation but I have not found it?
>  
> Where could I find it? I'm working on a Java Environment for Analysis and
> Alignment of Sequences!
>  
> Thanks,
> Anderson Moura - Brazil
> 
> 
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==================================================================
Sylvain Foisy, Ph. D.
Directeur - operations / Project Manager
BioneQ - Reseau quebecois de bio-informatique
U. de Montreal / Genome-Quebec

Adresse postale:

Departement de biochimie
Pavillon principal
2900, boul. Édouard-Montpetit
Montréal (Québec) H3T 1J4

Tel: (514) 343-6111 x.2545
Fax: (514) 343-7759
Courriel: sylvain.foisy at bioneq.qc.ca
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