[Biopython-dev] DendroPy is now BSD-licensed (was: [Nexml-discuss] NexML schema question)

Eric Talevich eric.talevich at gmail.com
Thu Oct 21 02:41:19 UTC 2010


About two months ago, Jeet Sukumaran mentioned on the NeXML-discuss mailing
list that he would be willing to relicense DendroPy, an excellent
phylogenetics library for Python, from GPL to the more permissive BSD

And shortly thereafter, he did:

For those just tuning in, DendroPy supports tree I/O in the NeXML format,
but not phyloXML; Biopython supports phyloXML but not NeXML. Since the
licenses are now compatible, we could probably make good use of Jeet's NeXML
parsing code at the very least. Unfortunately, as evidenced by my two-month
delay, I don't really have the leeway to do the integration myself this
semester. But here's a heads-up anyway.

Relatedly, Jaime Huerta Cepas (author of ETE, a Python Environment for Tree
Exploration) indicated interest in generating phyloXML and NeXML parsers
from XSD schemas -- another one to keep an eye out for.


---------- Forwarded message ----------
From: Jeet Sukumaran <jeet at ku.edu>
Date: Wed, Sep 22, 2010 at 12:51 PM
Subject: Re: [Nexml-discuss] NexML schema question
To: Eric Talevich <eric.talevich at gmail.com>
Cc: Jaime Huerta Cepas <jhcepas at gmail.com>, "NeXML-discuss (list)" <
nexml-discuss at lists.sourceforge.net>

Hi Eric,

Neither Mark nor I have any objections to releasing the DendroPy code to the
Biopython library under the BSD license. Not sure what legalities are
involved beyond saying "go for it", but if that's all it takes then "go for

-- jeet

On 9/22/10 10:49 AM, Eric Talevich wrote:

> On Sep 22, 2010, at 9:13 AM, Jaime Huerta Cepas wrote:
>> all I know is that Eric Talevich (the person who wrote the phyloXML parser
>> in biopython) seems to be working on this, as claimed in the biopython wiki.
>> But I don't think is ready yet.
> I took a crack at NeXML parsing a while ago, but it's nowhere near
> ready, and I don't expect to be able to work on it again for several
> more months.
> If you're looking for a currently usable library for working with
> NeXML (I didn't catch the rest of this discussion), DendroPy is nice.
> Its internal representation of tree objects isn't the same as
> Biopython's Bio.Phylo, and it's GPL, so we can't just plug it directly
> into Biopython (which uses a more permissive BSD-style license). But
> serializing a tree to Newick from Biopython and then parsing the
> Newick string in DendroPy, or the reverse, would give you some basic
> interoperability.
>     What I think is that XSD schemas could be automatically parsed to
>> generate parsers :) This would allow us to have a comprehensive and up to
>> date parser for the NexML schema that everyone can use.
> Sure! PhyloXML is defined by an XSD schema, too. With this approach,
> would it be possible for parsed phyloXML and NeXML tree objects to
> share a base class, so the same methods are available on each?
> -Eric

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