���U wrote: > Dear Sir, > > How to implement "Multiple Sequence Alignment" or "Phylogenetic > tree" in BioJava? > I cannot find any related function in online documents.... > > > > Jim
Hi Jim, There is no direct support for phylogenetic trees currently in BioJava. It would be a great thing to see added. We do have some support for alignments, via the org.biojava.bio.symbol.Alignment class. However, there are no well developed utilities or support code for making alignments realy easy to work with. In particular, Alignment needs modifying to allow easy addition/removal of sequences from the alignment, and we need to add an easy to use AlignmentSequence class so that you can annotate columns of an aligment as features. You can insert gaps into a view of an underlying ungapped sequence/symbol list using the GappedSymbolList and GappedSequence classes. You can then build an alignment object from these gapped views to get gapped alignemnts. The org.biojava.bio.dp package is a starting point for developing alignment algorithms. So far it only has alignments of one and two sequences to a model implemented, but the APIs do support symultaneous alignment of arbitrarily many sequences to a model. This is an area that needs work and documentation. Does anybody else on the list make alignments as part of their daily work? Matthew _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
