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 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

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.