[Biojava-l] Creating an alignment object

[Richard Holland]

BioJava itself cannot align sequences. It can only create objects that
are representations of alignments generated by third-party software. 

However, there is a third-party addon to BioJava called Strap, which can
actually do the alignment work itself from within your Java program and
return a BioJava alignment object that represents the results. It is
available for download, along with an example of how to use it, from
here:

 http://www.charite.de/bioinf/strap/biojavaInAnger_SequenceAligner.html

cheers,
Richard

On Thu, 2006-05-11 at 14:27 +0100, Nathan S. Haigh wrote:
> I'm new to Java and Biojava, but I've been having a play with writing and
> interface and some classes for an app I'd like to write in Java.
> 
> The part I'm playing around with at the moment deals with alignments and
> groups of alignment positions. What is the easiest/best way to create an
> alignment that I can then play around with and generate Locations from? A
> self contained working example would be great because as I said, I'm really
> new to java!
> 
> Cheers
> Nath
> 
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> Dr. Nathan S. Haigh
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416