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add an argument of OTT IDs to treat as tips

Status: Open.

#64 In OpenTreeOfLife/propinquity;

· mtholder opened on Dec 1, 2023

bogus info in cleaned trees step

Status: Open.

#61 In OpenTreeOfLife/propinquity;

· mtholder opened on Nov 7, 2023

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

Status: Open.

#60 In OpenTreeOfLife/propinquity;

· mtholder opened on Feb 14, 2023

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

Status: Open.

#58 In OpenTreeOfLife/propinquity;

· mtholder opened on Feb 17, 2021

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

Status: Open.

#56 In OpenTreeOfLife/propinquity;

· mtholder opened on Aug 10, 2020

Add License

Status: Open.

#55 In OpenTreeOfLife/propinquity;

· snacktavish opened on Jul 9, 2020

Add legumes to synth

Status: Open.

#54 In OpenTreeOfLife/propinquity;

· snacktavish opened on Jun 18, 2020

Propinquity fails with ott3.1 and ott3.2

Status: Open.

#51 In OpenTreeOfLife/propinquity;

· bredelings opened on Nov 6, 2019

compare_synthesis_outputs.py reported false conflicts due to incertae sedis placement

Status: Open.

#49 In OpenTreeOfLife/propinquity;

· bredelings opened on Oct 10, 2019

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

Status: Open.

#48 In OpenTreeOfLife/propinquity;

· mtholder opened on Oct 3, 2019

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

Status: Open.

#47 In OpenTreeOfLife/propinquity;

· mtholder opened on Apr 12, 2019

provide link to list of broken taxa from release notes

Status: Open.

#46 In OpenTreeOfLife/propinquity;

· kcranston opened on Oct 26, 2018