DendroPy 4.1.0 has been released!

5 views
Skip to first unread message

Jeet Sukumaran

unread,
Mar 16, 2016, 11:37:40 AM3/16/16
to DendroPy Announcements
DendroPy 4.1.0 has been released!!

Lots of new features, improvements, and bug fixes!

Major new features include:

    -   [SumTrees]: Tip dating! Tip-dating/non-contemporaneous tip age assignment using the "``--tip-ages``" argument (http://dendropy.org/programs/sumtrees.html#setting-the-node-ages-of-the-summary-trees).
    -   [SumTrees]: Collapse clades! "``--min-clade-freq``" applies to all summary targets (i.e., not just consensus trees, but user-specified as well as, e.g. MCCT trees).
    -   Phylogenetic community ecology statistics! Mean Pairwise Distance (MPD), Mean Nearest Taxon Distance (MNTD), Standardized Effect Size MPD and MNTD, equivalent to -1 * NRI and -1 * NTI (http://dendropy.org/primer/phylogenetic_distances.html#phylogenetic-community-statistics).
    -   The Protracted Speciation birth-death model: a Birth-Death process with explicit modeling of speciation-as-a-process rather than speciation-as-an-event by incorporating the lag between speciation initiation and speciation completion.
    -   Fast, flexible, and powerful tree and subtree cloning, extracting only nodes/taxa of interest (http://dendropy.org/primer/treemanips.html#extracting-trees-and-subtrees-from-an-existing-tree).

*LOTS* more happening under the hood! For more information:


Get it now with:

    $ sudo pip install --upgrade dendropy

or:
    $ sudo pip install -U dendropy


If you are working out of a 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).

Reply all
Reply to author
Forward
0 new messages