1.4 doesn't have anything for this, but 1.5 will do (the code is already in the head branch of CVS). Needleman-Wunsch and Smith-Waterman implementations are both in the org.biojava.bio.alignment package.
cheers, Richard On Wed, 2006-07-05 at 10:51 +0930, Michael Tran wrote: > 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 > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
