[Biojava-l] API for global alignments

[Michael Tran]

Hi
 
Looking for an API/class for doing global alignments (like a clustalW alignment) given a FASTA file.
 
The BioJava API 1.4 doesn't seem to have this.
 
org.biojava.bio.alignment <https://webmail.acpfg.local/org/biojava/bio/alignment/package-summary.html>  
Interfaces  
AlignmentElement <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AlignmentElement.html>  
ARAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/ARAlignment.html>  
EditableAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/EditableAlignment.html>  
QualitativeAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/QualitativeAlignment.html>  
UnequalLengthAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/UnequalLengthAlignment.html> 	
Classes  
AbstractULAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AbstractULAlignment.html>  
FlexibleAlignment <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/FlexibleAlignment.html>  
SimpleAlignmentElement <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/SimpleAlignmentElement.html> 	
Exceptions  
IllegalAlignmentEditException <https://webmail.acpfg.local/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/IllegalAlignmentEditException.html> 	

Any help appreciated.

Cheers,

MT

-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 4762 bytes
Desc: not available
URL: <http://lists.open-bio.org/pipermail/biojava-l/attachments/20060705/7fca4da5/attachment-0002.bin>