[Biojava-dev] Java API for Global Alignment

[Michael Tran]

Hi All,
 
Looking for a Java API to do global alignments (something like a clustalw alignment).
 
Looking at the BioJava API 1.4 (see below) does not appear to have such a class.
 
org.biojava.bio.alignment <https://mail.acpfg.com.au/org/biojava/bio/alignment/package-summary.html>  
Interfaces  
AlignmentElement <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AlignmentElement.html>  
ARAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/ARAlignment.html>  
EditableAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/EditableAlignment.html>  
QualitativeAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/QualitativeAlignment.html>  
UnequalLengthAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/UnequalLengthAlignment.html> 	
Classes  
AbstractULAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/AbstractULAlignment.html>  
FlexibleAlignment <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/FlexibleAlignment.html>  
SimpleAlignmentElement <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/SimpleAlignmentElement.html> 	
Exceptions  
IllegalAlignmentEditException <https://mail.acpfg.com.au/exchange/michael.tran/Drafts/RE:%20Biojava-l%20Digest,%20Vol%2042,%20Issue%2023.EML/IllegalAlignmentEditException.html> 	

Help is appreciated.
 
Cheers,
ST