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

Nick Matzke matzke at berkeley.edu
Mon Jul 20 19:56:18 UTC 2009

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.
> I gather you (Nick) are using this on ultrametric Newick trees


  - could
> you supply a sensibly sized example to use as a unit test? Initially
> this can be just to test Brad's patch to Bio.Nexus, but try and pick
> something you can build documentation examples around in future.

This is probable a reasonable size, a subset of my bigger tree.  (Just 
gymnosperms; times are in millions of years.)


I am using this as a test case in my own script, I have put some effort 
into reading up on Unittest but I don't quite get how it all fits 
together yet.

Another important case I will try and come up with is the results of 
pruning a tree, in my experience it is very easy to mess up the tree 
and/or branchlengths when pruning.

> Thanks,
> Peter

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

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