OpenTreeOfLife propinquity issues

OpenTreeOfLife / propinquity

make-based supertree pipeline

BSD 2-Clause "Simplified" License

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issues

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add an argument of OTT IDs to treat as tips

#64 mtholder opened 1 year ago
0
master to dev

#63 mtholder closed 1 year ago
0
master and main

#62 mtholder closed 1 year ago
0
bogus info in cleaned trees step

#61 mtholder opened 1 year ago
0
should be loud about input trees that are missing or pruned to nothing

#60 mtholder opened 1 year ago
0
Url update for custom synth download

#59 snacktavish closed 1 year ago
1
snakemake move has led to broken links to logs in the html documentation for each run

#58 mtholder opened 3 years ago
0
Modular snakemake

#57 mtholder closed 1 year ago
0
need to make sure forwarded IDs are not dropped from input trees

#56 mtholder opened 4 years ago
3
Add License

#55 snacktavish opened 4 years ago
0
Add legumes to synth

#54 snacktavish opened 4 years ago
0
Bump fossil higher

#53 mtholder closed 4 years ago
0
Fix ott files

#52 bredelings closed 5 years ago
1
Propinquity fails with ott3.1 and ott3.2

#51 bredelings opened 5 years ago
3
Fix fake collection script

#50 bredelings closed 5 years ago
0
compare_synthesis_outputs.py reported false conflicts due to incertae sedis placement

#49 bredelings opened 5 years ago
1
in annotations step, should trim non-terminal taxa's annotations back to tip in study

#48 mtholder opened 5 years ago
0
it might be interesting to look at using ASTRAL to solve subproblems

#47 mtholder opened 5 years ago
0
provide link to list of broken taxa from release notes

#46 kcranston opened 6 years ago
1
re-make failing because phylo_input/needs_updating has relative path

#45 bredelings closed 7 years ago
1
provide tree without extinct species

#44 kcranston opened 7 years ago
1
pipeline error if monophyly test fails

#43 kcranston closed 7 years ago
4
regrafting flagged taxa

#42 kcranston closed 7 years ago
0
Incertae sedis; more details on broken taxa

#41 kcranston closed 7 years ago
0
Incertae sedis

#40 mtholder closed 7 years ago
0
link directly to conflicting node in broken taxa lists

#39 kcranston opened 7 years ago
2
taxonomy forwards

#38 mtholder opened 7 years ago
0
Source-specific stats?

#37 josephwb opened 7 years ago
3
False report of no non-monophyletic taxa

#36 josephwb opened 7 years ago
5
Add synth_id to output docs; refactor compare script

#35 kcranston closed 7 years ago
0
Add synth_id to index.html and index.json

#34 kcranston closed 7 years ago
1
Merging work from mtholder fork

#33 kcranston closed 8 years ago
0
error in make clean

#32 kcranston closed 8 years ago
5
Broken links in output/

#31 jar398 closed 8 years ago
2
SHAs for phylesystem and collection shards

#30 jar398 closed 8 years ago
2
Unsupported node?

#29 josephwb closed 8 years ago
5
Update README.md

#28 josephwb closed 8 years ago
0
undocumented files in output directory

#27 jar398 opened 8 years ago
0
Merging work from development repo

#26 kcranston closed 8 years ago
0
perhaps tweak `make check` behavior

#25 mtholder opened 8 years ago
0
id repeated as a tip in subproblems

#24 mtholder closed 8 years ago
3
Associating paraphyletic taxa with the nodes that subtend them

#23 jar398 opened 8 years ago
0
It should be possible to put the opentree config someplace other than ~/.opentree

#22 jar398 closed 5 years ago
1
re-instate the grafted_supertree with user-friendly labels

#21 kcranston opened 8 years ago
1
grafted solutions doc promises list

#20 kcranston closed 8 years ago
1
diff tool across versions of the tree

#19 kcranston closed 7 years ago
1
merging from mtholder fork

#18 kcranston closed 8 years ago
0
changes used to create v5.0 synth tree + a few more commits from ben

#17 mtholder closed 8 years ago
0
Exemplification

#16 jar398 closed 8 years ago
3
OTU count needed for project progress reporting

#15 jar398 closed 8 years ago
5