New Release: DendroPy 3.9.0

[Jeet Sukumaran]

DendroPy 3.9.0 has been released!

http://pypi.python.org/pypi/DendroPy

Major new feature is built-in Phylogenetic Independent Contrasts (PIC)
analysis. Detailed tutorial available here:

http://packages.python.org/DendroPy/tutorial/phylogenetic_character_analyses.html

Other features/changes include:

- simplified contained coalescent (gene tree in species tree)
simulation:

http://packages.python.org/DendroPy/tutorial/treesims.html#contained-coalescent-trees

- simplified counting of deep coalescences:


http://packages.python.org/DendroPy/tutorial/treestats.html#number-of-deep-coalescences-when-embedding-one-tree-in-another-e-g-gene-species-trees

- clean-up of data i/o customization framework, with handy cut-and-
paste templates in the tutorials:

http://packages.python.org/DendroPy/tutorial/reading.html#nexus-newick

http://packages.python.org/DendroPy/tutorial/writing.html#nexus-and-newick

http://packages.python.org/DendroPy/tutorial/reading.html#fasta

http://packages.python.org/DendroPy/tutorial/writing.html#fasta

http://packages.python.org/DendroPy/tutorial/reading.html#phylip

http://packages.python.org/DendroPy/tutorial/writing.html#phylip

- plus the usual numerous bug fixes.

Detailed change log:

http://packages.python.org/DendroPy/changes.html