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Merge pull request #301: Link to lineage designation repo
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victorlin authored Jan 13, 2025
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Expand Up @@ -16,7 +16,7 @@ Our bioinformatic processing workflow can be found at [github.com/nextstrain/mpo
- masking several regions of the genome, including the first 1350 and last 6422 base pairs and multiple repetitive regions of variable length
- phylogenetic reconstruction using [IQTREE-2](http://www.iqtree.org/)
- ancestral state reconstruction and temporal inference using [TreeTime](https://github.com/neherlab/treetime)
- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/-/phylogenetic/defaults/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc...
- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/-/phylogenetic/defaults/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc. (defined by [mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation))

#### Underlying data
We curate sequence data and metadata from the [NCBI Datasets command line tools](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/),
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