Merge pull request #28 from nextstrain/add-clade-info-to-phylo-descri…

…ption

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

phylogenetic/defaults/description.md

@@ -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
@@ -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/