method getProgressiveAlignment in biojava
I have problems with using method I biojava in class alignments: getProgressiveAlignment(GuideTree<S,C> tree, Alignments.ProfileProfileAlignerType type, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix). I don't know what is Alignments.ProfileProfileAlignerType type and how to use it.
GuideTree: http://www.biojava.org/docs/api/org/biojava3/alignment/GuideTree.htmlAlignments.ProfileProfileAlignerType: http://www.biojava.org/docs/api/org/biojava3/alignment/Alignments.ProfileProfileAlignerType.htmlGapPenalty: http://www.biojava.org/docs/api/org/biojava3/alignment/template/GapPenalty.htmlSubstitutionMatrix: http://www.biojava.org/docs/api/org/biojava3/alignment/template/SubstitutionMatrix.html
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This is an enum to specify the algorithm used for the alignment. Using global and local alignment depends on the expected structure of alignment: large divergent sequences spanned by short highly similar regions, etc. You should start with some general reading: http://en.wikipedia.org/wiki/Sequence_alignment
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