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
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