[Biopython-dev] Bio.Nexus and internal node labels (Bug 2788)

Nick Matzke matzke at berkeley.edu
Wed Jul 29 04:33:46 UTC 2009

Peter wrote:
> On Tue, Jul 21, 2009 at 7:32 AM, Frank Kauff<fkauff at biologie.uni-kl.de> wrote:
>> Hi all,
>> Peter wrote:
>>> On Mon, Jul 20, 2009 at 8:13 PM, Nick Matzke wrote:
>>>> Hi all, here is my weekly update...
>>>> 1. Bug fix on Nexus.Tree class is working well so far.  Thanks Brad!!
>>> Cool. I haven't tried it personally though ;) Frank and/or Cymon - any
>>> comments regarding Brad checking this in? See Bug 2788 for details.
>> Not at all - you're most welcome. Thanks for dealing with it.
>> Frank
> Sounds like you should proably check in that fix then Brad :)
> Peter

Yeah, I used the revised module for a bunch more operations, including 
many of the tree methods.  No crashes or huge issues once I "got" how 
everything worked.

I did have to write my own methods for what should probably eventually 
be basic tree methods, like deep-copying the tree, subsetting the tree 
based on what occurs above a given node, etc.


Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

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Mailing address:
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"[W]hen people thought the earth was flat, they were wrong. When people 
thought the earth was spherical, they were wrong. But if you think that 
thinking the earth is spherical is just as wrong as thinking the earth 
is flat, then your view is wronger than both of them put together."

Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 
14(1), 35-44. Fall 1989.

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