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virus-evolution
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phylopipe
Pipeline to build a massive tree from global data
GNU General Public License v3.0
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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