DendroPy Change History

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.