Issues

• PhylogeneticDistanceMatrix results depend on object memory addresses

  bug
  jeetsukumaran/DendroPy#242 · Filter by author ryneches opened on Aug 31, 2026
  1

• Reroot at edge may assign edge labels incorrectly

  bug
  jeetsukumaran/DendroPy#216 · Filter by author terrycojones opened on Nov 1, 2024
  10

• Chore: Fix ResourceWarnings from tests

  enhancement
  jeetsukumaran/DendroPy#165 · Filter by author mmore500 opened on Apr 11, 2023

• Some examples in /docs/source/examples are broken

  enhancementinfrastructure
  jeetsukumaran/DendroPy#160 · Filter by author mmore500 opened on Apr 1, 2023

• Should Node.extract_subtree return Tree, not seed node, & copy annotations?

  enhancement
  jeetsukumaran/DendroPy#143 · Filter by author MordorianGuy opened on Sep 1, 2022

• resolve_polytomies could return number of polytomies resolved

  enhancement
  jeetsukumaran/DendroPy#126 · Filter by author hyanwong opened on Oct 7, 2020

• Test suite vanished from download tarball

  enhancementinfrastructure
  jeetsukumaran/DendroPy#122 · Filter by author tillea opened on Oct 8, 2019
  4

• dendropy.utility.error.UltrametricityError

  enhancement
  jeetsukumaran/DendroPy#121 · Filter by author nick-youngblut opened on Sep 19, 2019
  2

• accuracy of gene tree simlation

  question
  jeetsukumaran/DendroPy#120 · Filter by author zzbbf123 opened on Sep 6, 2019

• Preserve_underscores

  enhancement
  jeetsukumaran/DendroPy#112 · Filter by author wrightaprilm opened on Apr 23, 2019
  2

• MRCA algorithm can be faster

  enhancement
  jeetsukumaran/DendroPy#99 · Filter by author niemasd opened on Sep 11, 2018
  1

• Floating point error accumulation in contained coalescent trees

  enhancement
  jeetsukumaran/DendroPy#63 · Filter by author yasuiniko opened on Jul 13, 2016

• possible enhancement: retain edge identity when rerooting

  enhancement
  jeetsukumaran/DendroPy#54 · Filter by author mtholder opened on May 17, 2016
  1

• Maximum recursion depth error

  enhancement
  jeetsukumaran/DendroPy#52 · Filter by author ericmjl opened on May 13, 2016
  8

• Feature request: Writing to JSON schema

  enhancement
  jeetsukumaran/DendroPy#46 · Filter by author Zsailer opened on Mar 31, 2016
  14

• Parsing NEXUS trees with undefined taxon labels does not raise error

  enhancement
  jeetsukumaran/DendroPy#37 · Filter by author jeetsukumaran opened on Oct 5, 2015
  1

• Common Ancestors age strategy for --set-edges

  enhancement
  jeetsukumaran/DendroPy#32 · Filter by author nitishnarula opened on Sep 11, 2015

• Ordered Parsimony

  enhancement
  jeetsukumaran/DendroPy#25 · Filter by author mccannj9 opened on Aug 12, 2015
  1