[BioPython] Distance Matrix Parsers

[Chris Lasher]

> I likewise didn't know about the Bio::Matrix::PhylipDist module.
> Personally, I would opt for a Matrix Object (since this is Python a
> OO language) and store it internally as a nested list. That way you
> have the best of both worlds. The next question is the object
> hierarchy. Here I would opt for a top level Matrix class (or module)
> and then subclass that under Phylo. So, something like this:
>
> Bio.Matrix
> Bio.Phylo.Matrix

So is this more appropriate than Bio.Matrix.Phylo? A phylogenetic
matrix is a type of matrix, so that hierarchy is immediately
appealing, however, a phylogenetic matrix is not of much use in and of
itself, so I can see the argument that it should be placed in a
phylogeny package (which we have yet to write but as mentioned
earlier, could be very useful).

> and maybe things like the following (which isn't used/followed much
> here in BioPython)
>
> Bio.Phylo.IO
> Bio.Phylo.Parsers.PhylipDist
> Bio.Phylo.Parsers.Newick
> Bio.Phylo.Parsers.Nexus
>
> And/or have
> Bio.Phylo.Matrix.IO that uses the PhylipDist parser.

This is very very good, in my opinion. Thanks for doing the
heavy-lifting of the brainwork on this! =-)

> The next big question is what should Bio.Phylo.IO return? For
> inspiration, we might want to look at Mesquite <http://
> mesquiteproject.org/mesquite/mesquite.html>.

I must give a better look at this site before commenting, but once
again, thanks for bringing this to my awareness! What a helpful past
couple of emails. I will be out for the weekend but will think more
about this.

As a sidenote, should this discussion be moved to biopython-dev or is
it fine here?

Thanks again Marc,
Chris