[Biopython-dev] GSoC final update: PhyloXML for Biopython

[Eric Talevich]

Hi all,

Here's a final changelog for Aug. 10-14:

- Added a 'terminal' argument to the find() method on BaseTree.Tree, for
  filtering internal/external nodes. This makes get_leaf_nodes() a trivial
  function, and total_branch_length is pretty simple too.

- Updated the example phyloXML files to v1.10 schema-compliant copies from
  phyloxml.org; couple bug fixes.

- Removed the project's README.rst file, so Bio/PhyloXML/ is no longer
  controlled by Git. I'll merge any useful information from there into the
  Biopython wiki documentation.

- Pulled the Biopython 1.51 release into my master branch, and merged that
  into the phyloxml branch, so this branch (and the required GSoC patch
  tarball) will apply cleanly to the publicly released Biopython 1.51 source
  tree.

- Documented most of what's been done on the Biopython wiki:
    http://www.biopython.org/wiki/PhyloXML
    http://www.biopython.org/wiki/TreeIO
    http://www.biopython.org/wiki/Tree


*Future plans*

There are a few tangential projects that deserve more attention over the
next few months, and I'm going to create separate Git branches for each of
them, to make it easier to share:

    - Port the Newick tree parser and methods from Bio.Newick to Bio.Tree
and
      TreeIO.

    - Improve the graph drawing and networkx integration

    - BioSQL adapter between Bio.Tree.BaseTree and PhyloDB tables

    - Possibly, play with other tree representations -- nested-set, as
PhyloDB
      does, and relationship matrix, which could bring NumPy into play (in a
      separate Bio.Tree.Matrix module)


Finally, massive thanks to Brad and Christian for mentoring, Hilmar for
overseeing the whole project, Peter and the Biopython folks for their
guidance, and the various BioPerl monks and BioRubyists who shared their
wisdom.

All the best,
Eric
https://www.nescent.org/wg_phyloinformatics/PhyloSoC:Biopython_support_for_parsing_and_writing_phyloXML