Issues

• add an argument of OTT IDs to treat as tips

  OpenTreeOfLife/propinquity#64 · Filter by author mtholder opened on Dec 1, 2023

• bogus info in cleaned trees step

  OpenTreeOfLife/propinquity#61 · Filter by author mtholder opened on Nov 7, 2023

• should be loud about input trees that are missing or pruned to nothing

  OpenTreeOfLife/propinquity#60 · Filter by author mtholder opened on Feb 14, 2023

• snakemake move has led to broken links to logs in the html documentation for each run

  OpenTreeOfLife/propinquity#58 · Filter by author mtholder opened on Feb 17, 2021

• need to make sure forwarded IDs are not dropped from input trees

  OpenTreeOfLife/propinquity#56 · Filter by author mtholder opened on Aug 10, 2020
  3

• Add License

  OpenTreeOfLife/propinquity#55 · Filter by author snacktavish opened on Jul 9, 2020

• Add legumes to synth

  OpenTreeOfLife/propinquity#54 · Filter by author snacktavish opened on Jun 18, 2020

• Propinquity fails with ott3.1 and ott3.2

  OpenTreeOfLife/propinquity#51 · Filter by author bredelings opened on Nov 6, 2019
  3

• compare_synthesis_outputs.py reported false conflicts due to incertae sedis placement

  OpenTreeOfLife/propinquity#49 · Filter by author bredelings opened on Oct 10, 2019
  1

• in annotations step, should trim non-terminal taxa's annotations back to tip in study

  OpenTreeOfLife/propinquity#48 · Filter by author mtholder opened on Oct 3, 2019

• it might be interesting to look at using ASTRAL to solve subproblems

  OpenTreeOfLife/propinquity#47 · Filter by author mtholder opened on Apr 12, 2019

• provide link to list of broken taxa from release notes

  OpenTreeOfLife/propinquity#46 · Filter by author kcranston opened on Oct 26, 2018
  1

• provide tree without extinct species

  OpenTreeOfLife/propinquity#44 · Filter by author kcranston opened on Jun 23, 2017
  1

• link directly to conflicting node in broken taxa lists

  OpenTreeOfLife/propinquity#39 · Filter by author kcranston opened on Mar 10, 2017
  2

• taxonomy forwards

  OpenTreeOfLife/propinquity#38 · Filter by author mtholder opened on Feb 22, 2017

• Source-specific stats?

  OpenTreeOfLife/propinquity#37 · Filter by author josephwb opened on Dec 22, 2016
  3

• False report of no non-monophyletic taxa

  OpenTreeOfLife/propinquity#36 · Filter by author josephwb opened on Dec 17, 2016
  5

• undocumented files in output directory

  OpenTreeOfLife/propinquity#27 · Filter by author jar398 opened on Aug 16, 2016

• Associating paraphyletic taxa with the nodes that subtend them

  OpenTreeOfLife/propinquity#23 · Filter by author jar398 opened on Jun 22, 2016

• re-instate the grafted_supertree with user-friendly labels

  OpenTreeOfLife/propinquity#21 · Filter by author kcranston opened on May 14, 2016
  1