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jeromekelleher
/
sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Mutations reported in copying pattern incorrect
#92
jeromekelleher
opened
1 year ago
0
Three + parents broken in report
#91
jeromekelleher
closed
1 year ago
1
Validate by chunks
#90
jeromekelleher
closed
1 year ago
0
Change _copying_table to be horizontal & colour
#89
hyanwong
closed
1 year ago
0
Add CLI for annotating recombinants with breakpoint info
#88
jeromekelleher
closed
1 year ago
0
Fix missing nodes arg
#87
jeromekelleher
closed
1 year ago
0
Reversion push code needs to deal with recombinants
#86
jeromekelleher
opened
1 year ago
2
Create RecombinantAncestry.ipynb
#85
hyanwong
closed
1 year ago
0
Use imputated pango if available
#84
jeromekelleher
closed
1 year ago
0
Fix bug in annotations
#83
jeromekelleher
closed
1 year ago
0
Add postprocess function to update "flagged" node times
#82
jeromekelleher
opened
1 year ago
0
Ability not to filter out sites on intersection
#81
hyanwong
closed
1 year ago
3
Node 1240908 incorrectly placed in upgma-full-md-30-mm-3-2021-06-30.ts.tsz
#80
jeromekelleher
opened
1 year ago
1
Some branch lengths systematically too long
#79
jeromekelleher
opened
1 year ago
0
Don't import tsconvert
#78
jeromekelleher
closed
1 year ago
0
Ways to correct "myopic" tree building
#77
hyanwong
opened
1 year ago
1
Site utils
#76
jeromekelleher
closed
1 year ago
0
Add nextstrain colours
#75
hyanwong
closed
1 year ago
2
Functions to extract the nextstrain nexus files
#74
hyanwong
closed
1 year ago
0
Add cophylogeny notebook
#73
hyanwong
closed
1 year ago
2
Rename nextstrain JSON functions to "nextclade"
#72
hyanwong
closed
1 year ago
0
Adds genes to plots
#71
jeromekelleher
closed
1 year ago
0
Nextstrain tree only contains intergenic mutations
#70
jeromekelleher
opened
1 year ago
2
Lineage imputation
#69
a-ignatieva
closed
1 year ago
1
Plot of dN/dS along the genome
#68
jeromekelleher
opened
1 year ago
1
Add private mutations to reports
#67
jeromekelleher
closed
1 year ago
0
Lineage imputation and sample subgraph plots
#66
a-ignatieva
closed
1 year ago
5
Nextstrain utilities
#65
jeromekelleher
closed
1 year ago
0
Add genes to plots
#64
jeromekelleher
closed
1 year ago
0
Generalise inspection code
#63
jeromekelleher
closed
1 year ago
0
Improvements to recombinant handling
#62
jeromekelleher
closed
1 year ago
0
Remove extra code that snuck in
#61
jeromekelleher
closed
1 year ago
0
Fix error in recombinants per day plot
#60
jeromekelleher
closed
1 year ago
0
recombinants plot broken
#59
jeromekelleher
closed
1 year ago
0
Inspect recombinant
#58
jeromekelleher
closed
1 year ago
0
Minor tweaks to utils
#57
jeromekelleher
closed
1 year ago
0
Fixup some broken analysis code by change of metadata
#56
jeromekelleher
closed
1 year ago
0
Revert to scipy-based UPGMA tree
#55
jeromekelleher
closed
1 year ago
0
Local tsinfer
#54
jeromekelleher
closed
1 year ago
1
Update metadata for added nodes.
#53
jeromekelleher
closed
1 year ago
0
Build local trees using maximum parismony
#52
jeromekelleher
closed
1 year ago
0
Recombinant lineages report
#51
jeromekelleher
closed
1 year ago
0
More utils
#50
jeromekelleher
closed
1 year ago
0
Add utils
#49
jeromekelleher
closed
1 year ago
0
Record spike dropouts for QC
#48
jeromekelleher
opened
1 year ago
1
Don't allow non-samples to be reversion pushes
#47
jeromekelleher
closed
1 year ago
0
Use threads when reading alignments
#46
jeromekelleher
opened
1 year ago
0
Add option to compress daily output
#45
jeromekelleher
opened
1 year ago
0
Rough version of max-daily-samples
#44
jeromekelleher
closed
1 year ago
0
bRecombinant nodes
#43
jeromekelleher
closed
1 year ago
0
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