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neherlab
/
nextclade_data_workflows
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neherlab/nextclade_data_workflows Issues
Rename `gene` to `cds`
Updated
7 months ago
Don't count nucleotides 0-100 towards divergence
Updated
a year ago
ENH: Attach recombinants at most recent common ancestor
Updated
a year ago
ENH: Put all recombinants on single branch from root
Closed
a year ago
ENH: Soft mask 26577 (M:19) instead of hard mask
Closed
a year ago
colour omicron in tree properly
Closed
a year ago
Use hand curated list of high quality Omicron sequences
Closed
a year ago
Unmask S:95
Closed
a year ago
Include GISAID data provenance
Closed
a year ago
Exclude S:142G sequences within Delta as outliers
Closed
a year ago
Don't pull GISAID sequences into output
Closed
a year ago
ENH: Add recombinants back in, as subtree connected to root
Closed
a year ago
Comments count
1
ENH: Manual overwrite of lineage mutations
Closed
a year ago
Comments count
1
Use pango defining mutations to improve synthetic lineage curation
Updated
a year ago
Comments count
1
Prohibit reversions by default, make allowlist for real reversions
Updated
a year ago
Comments count
1
ENH: Add date of designation to SC2 build for pango lineages
Closed
a year ago
Comments count
1
BUG: 28370 not overwritten with `-` but `T` 28371 -> T in BF.7
Closed
a year ago
Comments count
1
MPXV: Remove duplicates (after masking) to reduce tree size
Updated
a year ago
Comments count
1
Include XBB in 21L build to not call BJ.1
Closed
a year ago
Comments count
1
ENH: Remove real sequences from Nextclade build
Closed
a year ago
Comments count
1
ENH: Make BA.2 build side-product of main build
Closed
a year ago
Comments count
1
ENH: Allow recombinant sublineages to be present
Closed
a year ago
Comments count
1
ENH: Add escape score etc as colorings
Updated
a year ago
Comments count
1
ENH: Build proper tree for XBB.1.5 rather than the simplistic current one
Closed
a year ago
Comments count
1
MPXV: Add reversions to virus_properties in B.1 build
Updated
2 years ago
Auto generate constraint.nwk from pango alias file, allow additional resolution
Updated
2 years ago
Request: Add vaccine strains and clade defining viruses to NextClade flu dataset
Updated
3 years ago
Filter out Egypt/Iraq due to often bad quality
Closed
3 years ago