Issues
- 2
Add Nextstrain clade labels to node metadata
#223 opened - 2
- 0
- 0
Paragraph on trade-offs between removing time travellers and capturing early stages of an outbreak
#220 opened - 1
QC based on branch length
#217 opened - 1
Variant-specific mutational spectra
#216 opened - 13
- 0
- 2
Identify recombinants which we are reasonably certain of, which have not previously been detected
#213 opened - 0
Add script to run MAFFT on cluster
#211 opened - 1
- 4
- 3
New PANGO recombinants
#207 opened - 2
- 0
New cophylogeny
#205 opened - 0
Cite pyfaidx
#203 opened - 0
Correct funding source for Ben Jeffery
#202 opened - 0
Investigating false positives
#199 opened - 2
Fill out the README file in this repo
#198 opened - 0
Cite recombinhunt preprint
#195 opened - 0
Cite recombination opinion piece
#194 opened - 0
"Strain" terminology
#193 opened - 4
Change mutation notation?
#183 opened - 1
Update caption for s4
#182 opened - 6
Add forward refs to FP section
#181 opened - 4
- 7
Minor visual improvements for figs 1 & 6
#176 opened - 3
Use standard terminology for inherited state
#173 opened - 1
- 0
Clarify edge parents
#165 opened - 0
Define mutation process
#164 opened - 1
Section 2.5 query for Katherine
#161 opened - 0
Update LS HMM section
#160 opened - 38
- 1
Tackle False positives
#155 opened - 0
Migrate s4.7 notebooks to sc2ts repo
#153 opened - 1
Move nextstrain.py to paper repo
#151 opened - 1
- 3
Checklist before publishing: scan for FIXMEs
#142 opened - 0
Checklist before publishing: turn on URLs
#141 opened - 1
Fig S3 caption out of date
#136 opened - 1
Fig S1 missing dates
#135 opened - 31
Tweaks for method overview figure
#131 opened - 13
- 0
Pango recombinant notebook slightly wrong
#116 opened - 0
- 0
Finish breakpoint intervals figure
#109 opened - 8
Issues with backbone phylo section
#102 opened - 1
- 0
Finalise pango imputation methods
#94 opened