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Issues list

add an argument of OTT IDs to treat as tips
#64 opened Dec 1, 2023 by mtholder
bogus info in cleaned trees step
#61 opened Nov 7, 2023 by mtholder
should be loud about input trees that are missing or pruned to nothing
#60 opened Feb 14, 2023 by mtholder
snakemake move has led to broken links to logs in the html documentation for each run
#58 opened Feb 17, 2021 by mtholder
need to make sure forwarded IDs are not dropped from input trees
#56 opened Aug 10, 2020 by mtholder
3
Add License
#55 opened Jul 9, 2020 by snacktavish
Add legumes to synth
#54 opened Jun 18, 2020 by snacktavish
Propinquity fails with ott3.1 and ott3.2
#51 opened Nov 6, 2019 by bredelings
3
compare_synthesis_outputs.py reported false conflicts due to incertae sedis placement
#49 opened Oct 10, 2019 by bredelings
1
in annotations step, should trim non-terminal taxa's annotations back to tip in study
#48 opened Oct 3, 2019 by mtholder
it might be interesting to look at using ASTRAL to solve subproblems
#47 opened Apr 12, 2019 by mtholder
provide link to list of broken taxa from release notes
#46 opened Oct 26, 2018 by kcranston
1
provide tree without extinct species
#44 opened Jun 23, 2017 by kcranston
1
link directly to conflicting node in broken taxa lists
#39 opened Mar 10, 2017 by kcranston
2
taxonomy forwards
#38 opened Feb 22, 2017 by mtholder
Source-specific stats?
#37 opened Dec 22, 2016 by josephwb
3
False report of no non-monophyletic taxa
#36 opened Dec 17, 2016 by josephwb
5
undocumented files in output directory
#27 opened Aug 16, 2016 by jar398
perhaps tweak make check behavior
#25 opened Jun 28, 2016 by mtholder
Associating paraphyletic taxa with the nodes that subtend them
#23 opened Jun 22, 2016 by jar398
re-instate the grafted_supertree with user-friendly labels
#21 opened May 14, 2016 by kcranston
1
ProTip! Exclude everything labeled bug with -label:bug.