[Biojava-l] Multiple Sequence Alignment Viewer

[Thomas Down]

Once upon a time, Nathan Whitehouse wrote:
> 
>   I've used biojava on and off for some time, and I've
> always found it useful.
> 
>   I'm not sure how to proceed with my current problem,
> though I'm sure someone has done it already.
>   
>   I basically need a way to visualize a set of
> sequences which need to be aligned.
> 
>   Can anybody point me in the right direction on this?
>   Is there an easy tool to visualize multiple
> alignments? 

BioJava includes a sequence GUI toolkit which could certainly
be used to write an effective alignment viewer.  If you're
interested in going down this route, take a look at the
org.biojava.bio.gui.sequence package: a combination of
AlignmentRenderer and SymbolSequenceRenderer should give
a basic alignment viewer.

If you're looking for an off-the-shelf application, I don't
know of any general biojava-based solutions.  But you might
find JalView useful:

     http://www2.ebi.ac.uk/~michele/jalview/contents.html


Thomas.