[Biopython-dev] Phylo: support for JSON trees

Fabio Zanini fabio.zanini at fastmail.fm
Wed Dec 9 21:12:41 UTC 2015

Hi all,

I've been working with phylogenetic trees for a few years and found it
very convenient to convert Bio.Phylo trees to/from JSON, e.g.

{'name': 'root', 'children': [
  {'name': 'leaf1', 'branch_length': 0.01, children: []},
  {'name': 'leaf2', 'branch_length': 0.02, children: []}]

I would like to implement such import/export functions into Bio.Phylo if
there is interest. Because Python has a JSON parser already, it's like
50 lines of code altogether.

The main arguments in favour of this are:
- *JSON is standard for the web*, and the web is where all is moving
(Jupyter, bokeh, but also specific tree-oriented web apps such as
- embedding metadata is trivial (just add more keys to those dicts!)

How's that sound, shall I make a github PR?


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