-------------
New or Updated Features
^^^^^^^^^^^^^^^^^^^^^^^
- [SumTrees]: 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]: "``--min-clade-freq``" applies to all summary targets (i.e., not just consensus trees, but user-specified as well as, e.g. MCCT trees).
- 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).
- Neighbor-joining and UPGMA trees (http://dendropy.org/primer/phylogenetic_distances.html#generating-distance-trees-from-a-phylogeneticdistancematrix-object).
- The new (actually, warmed-over) PhylogeneticDistanceMatrix to manage various "within-tree" distances, such patristic distances, or the ecological statistics described below (http://dendropy.org/primer/phylogenetic_distances.html#creating-a-phylogeneticdistancematrix-object).
- Added phylogenetic community ecology statistic calculations: 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).
- Added DataTable class to manage community ecology (as well as more general classes of) data.
- Implementation of the Protracted Speciation 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.
- NEWICK terminating semicolon requirement relaxation.
- Some more refined node filtering/dropping.
- Return list of nodes dropped when filtering out leaves.
- Force max/min ages when calculating node ages; and beginning of support for setting node ages by function.
- Implementation of Tree.find_nodes() to return collection of nodes that match instaed of just the first one.
Bug Fixes
^^^^^^^^^
- Handle sequence comparison where there are no non-ignored sites in common.
- Update string type checking to handle unicode etc. under Python 2.
- Exclusion of trees from data set reads actually works.
- Actually implement symbol to state (alphabet) identity coercion in derived classes.
- Pop out inner classes to enable pickling.
- Several bugs, mostly caused by leftovers of DendroPy3 code.
- Made group_ranges work properly with unordered iterables.
- Make PHYLIP writing work correctly with missing taxa.