virus-evolution phylopipe issues

virus-evolution / phylopipe

Pipeline to build a massive tree from global data

GNU General Public License v3.0

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issues

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Consider date uploaded to CLIMB when adding to tree

#23 rmcolq closed 2 years ago
0
Citation

#22 ptlcc opened 3 years ago
1
Use mutation list to generate VCF for usher

#21 rmcolq opened 3 years ago
0
Move s3 out of phylopipe

#20 rmcolq closed 3 years ago
0
Investigate lineages in tree which are split

#19 rmcolq opened 3 years ago
0
Update why_excluded column at each step again

#18 rmcolq closed 3 years ago
1
Filter for specific ambiguous sites before downsampling

#17 rmcolq closed 3 years ago
0
Add to mask sites

#16 rmcolq closed 3 years ago
0
Is pillar_2 deprecated?

#15 mattloose closed 3 years ago
5
Make private civet metadata output containing `adm2`

#14 rmcolq closed 3 years ago
1
Investigate UK sequences missing `phylotype` assignment but containing `uk_lineage`

#13 rmcolq closed 3 years ago
3
Investigate adding IQTree optimization post-usher

#12 rmcolq opened 3 years ago
1
Extract max parsimony placement number from usher and flag in metadata

#11 rmcolq closed 3 years ago
0
Off by one coordinates in usher training

#10 rmcolq closed 3 years ago
0
Remove sticky out branches

#9 rmcolq opened 3 years ago
1
Rescale integer branch lengths after usher

#8 rmcolq closed 3 years ago
0
Handle single quotes in nexus annotations

#7 rmcolq closed 3 years ago
0
Debug why publishing is no SO SLOW

#6 rmcolq closed 3 years ago
1
Breaks when all sequences are already in tree and try to update with usher_expand_tree

#5 rmcolq closed 3 years ago
1
Update choice of lineage splits with appropriate outgroups

#4 rmcolq opened 3 years ago
0
Compare outputs to phylopipe1

#3 rmcolq closed 3 years ago
0
Update to force some sequences to be added

#2 rmcolq closed 3 years ago
1
Pull aliases from github

#1 rmcolq closed 3 years ago
0