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Switch to using pathoplexus for nextclade #323

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770e292
feat(phylo/clade-i): Lift OPG gene names from all-clades build to cla…
corneliusroemer Mar 18, 2025
41a7f30
Switch off timetree for clade I as it doesn't work given the range o…
corneliusroemer Mar 18, 2025
e3be330
Use accession not accessionVersion for stability
corneliusroemer Mar 20, 2025
57c48f2
Remove versions from known duplicates
corneliusroemer Mar 20, 2025
c1bf3c6
parallelized deduplicate
corneliusroemer Mar 20, 2025
fae30b1
weights
corneliusroemer Mar 22, 2025
824b6c2
Better masking of clade I issues in all-clades tree
corneliusroemer Mar 26, 2025
dd0a687
More fine grained sampling and exclusions
corneliusroemer Mar 26, 2025
5ea0d32
Few more changes
corneliusroemer Mar 26, 2025
cedd253
Fix ambiguous date format for augur filter
corneliusroemer Apr 2, 2025
8053a8b
Add more known duplicates
corneliusroemer Apr 10, 2025
07a9c8b
Add more known duplicates
corneliusroemer Apr 19, 2025
df0fc48
Use masked alignment for refine (branch lengths)
corneliusroemer Apr 24, 2025
9014abb
Fix build url, thanks @chaoran-chen for the spot
corneliusroemer Apr 25, 2025
ffd63af
Fix deprecation of --output
corneliusroemer Aug 21, 2025
05dae74
Preparing for new lineages
corneliusroemer Aug 21, 2025
bd27f7c
Add clades.tsv and color ordering for new lineage designations
corneliusroemer Sep 7, 2025
b5dd32e
Add new lineages to config.yaml
corneliusroemer Sep 7, 2025
35202cf
Add new includes
corneliusroemer Sep 7, 2025
7e86161
Add more includes and excludes
corneliusroemer Sep 7, 2025
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5 changes: 3 additions & 2 deletions nextclade/README.md
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Expand Up @@ -36,8 +36,9 @@ nextstrain view auspice/
```bash
cd ~/code
cp mpox/nextclade/datasets/all-clades/tree.json nextclade_data/data/nextstrain/mpox/all-clades/tree.json
cp mpox/nextclade/datasets/clade-iib/tree.json nextclade_data/data/nextstrain/mpox/clade_iib/tree.json
p mpox/nextclade/datasets/lineage-b.1/tree.json nextclade_data/data/nextstrain/mpox/lineage-b.1/tree.json
cp mpox/nextclade/datasets/clade-iib/tree.json nextclade_data/data/nextstrain/mpox/clade-iib/tree.json
cp mpox/nextclade/datasets/clade-i/tree.json nextclade_data/data/nextstrain/mpox/clade-i/tree.json
cp mpox/nextclade/datasets/lineage-b.1/tree.json nextclade_data/data/nextstrain/mpox/lineage-b.1/tree.json
```

## Configuration
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