DendroPy Change History

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.