diff --git a/phylogenetic/defaults/description.md b/phylogenetic/defaults/description.md index c8ac650..7508f3b 100644 --- a/phylogenetic/defaults/description.md +++ b/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/