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Update phylo description.md with note about clade annotation [#25] #28

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Dec 16, 2024
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Update phylo description.md with note about clade annotation [#25] #28

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22 changes: 22 additions & 0 deletions phylogenetic/defaults/description.md
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Expand Up @@ -23,6 +23,26 @@ We curate sequence data and metadata from NCBI as starting point for
our analyses. We gratefully acknowledge the large contribution of over
500 sequences from Hill, et al.

#### Clade annotation

The clades we annotate on the yellow fever trees (Clades I-VII) are
roughly equivalent with the following genotypes as described in
[Mutebi et al.][] (J Virol. 2001 Aug;75(15):6999-7008) and [Bryant et
al.][] (PLoS Pathog. 2007 May 18;3(5):e75).

| Clade | Genotype |
|-----------|---------------------|
| Clade I | Angola |
| Clade II | East Africa |
| Clade III | East/Central Africa |
| Clade IV | West Africa I |
| Clade V | West Africa II |
| Clade VI | South America I |
| Clade VII | South America II |

(N.b., this table is available as a TSV in this repo, at
`nextclade/defaults/clade-to-genotype.tsv`.)

---

Screenshots may be used under a [CC-BY-4.0 license][] and attribution
Expand All @@ -33,4 +53,6 @@ to nextstrain.org must be provided.
[IQTREE-2]: http://www.iqtree.org/
[Nextclade]: https://nextstrain.org/fetch/data.clades.nextstrain.org/v3/nextstrain/yellow-fever/prM-E/2024-11-05--09-19-52Z/tree.json
[TreeTime]: https://github.com/neherlab/treetime
[Mutebi et al.]: https://pubmed.ncbi.nlm.nih.gov/11435580/
[Bryant et al.]: https://pubmed.ncbi.nlm.nih.gov/17511518/
[CC-BY-4.0 license]: https://creativecommons.org/licenses/by/4.0/
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