[Biojava-l] Functions Requirement...

[Matthew Pocock]

ŞüĞU 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