CHANGES.rst

Release 4.5.2

• Support for user-specified random seed in RaXML wrapper (thanks @NoahAmsel)
• MUCH faster label lookup (thanks Sam Nicholls / @SamStudio8 !)
• Faster birth-death tree generation (thanks @NicolaDM !)
• Storage of supplemental NEXUS blocks
• Fix type: "PhylogeneticIndependentConstrasts" => "PhylogeneticIndependentContrasts"

Release 4.4.0

• Calculation of birth-death likelihoods.
• Bipartitions inherit rooting state of trees.
• Patristic paths between tips can be tracked in PatristicDistanceMatrix.
• Character column metadata annotations now actually possible.
• Standard character matrix defaults to 0-9 alphabet instead of just 01.
• Reorganization of package directory: from "$HOME/dendropy" and "$HOME/dendropy/test" to more modern "$HOME/src/dendropy" and "$HOME/tests" respectively.

Release 4.3.0

• [SumTrees]: Important bugfix in tracking splits on consensus tree from rooted trees: previously it was possible for a split on the consensus tree to be ignored, resulting in a null (0) edge length and no (0.0) support.
• Added sumlabels.py application.
• Birth-death tree (dendropy.model.birth_death_tree) now allows for preservation of extinct tips.
• Improved performance of character subset export

Release 4.2.0

• 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.

Release 4.1.0

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.

Release 4.0.3

Bug Fixes

• [SumTrees]: propagate -f/--frequency option to underlying summarization engine.
• [SumTrees]: -v/--ultrametricity-precision option takes numeric value.
• Exporting of characters from matrix suppresses cloned character subset definitions.

Release 4.0.2

Bug Fixes

• Adjustment of child edge lengths when collapsing basal bifurcations.

Release 4.0.1

Bug Fixes

• Fix for installing using in virtual environments under virtualenv.