DendroPy 4.2.0 has been released!

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Jeet Sukumaran

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Dec 28, 2016, 1:42:48 PM12/28/16
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DendroPy 4.2.0 has been released!!

Highlights:

- 0 branch lengths assigned to randomly resolved polytomies.
- Explicitly set rooting for NJ and UPGMA trees.
- Faster pruning (kyungtaekLIM)
- Fix nesting bug in raised KeyError in basemodel.AnnotationSet.__deepcopy__ (Steve Bond)
- Catch edge case during deepcopy when Edge object has no _annotations (Steve Bond)
- Optimizations and fixes for various population genetic calculations (Andrew Guy)
- newickreader: Parse jplace style edge numbering. (Ben J Woodcroft)
- Calculate probability of gene tree(s) in species trees under the Multispecies Coalescent model.
- New approaches to calculate distances between unlabeled trees of different sizes: ``dendropy.profiledistance`` and ``dendropy.calculate.treecompare.TreeShapeKernel``.
- When parsing Newick/NEXUS, allow for internal node labels to be associated with either nodes or edges.

For more information:

http://dendropy.org

Get it now with:

$ sudo pip install --upgrade dendropy

or:
$ sudo pip install -U dendropy

You can install directly from the main GitHub repository using:

$ pip install git+https://github.com/jeetsukumaran/DendroPy.git

or:

$ pip install git+git://github.com/jeetsukumaran/DendroPy.git

Or, if you are working out of a local Git repo:

$ git pull origin
$ python setup.py build
$ sudo python setup.py develop

(note: ``sudo`` should be used only if you are installing system-wide using your system Python).

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