diff --git a/phylogenetic/defaults/description.md b/phylogenetic/defaults/description.md index a0486df..c363889 100644 --- a/phylogenetic/defaults/description.md +++ b/phylogenetic/defaults/description.md @@ -13,4 +13,26 @@ We curate sequence data and metadata from NCBI as starting point for our analyse * [data.nextstrain.org/files/workflows/dengue/sequences_denv4.fasta.zst](https://data.nextstrain.org/files/workflows/dengue/sequences_denv4.fasta.zst) * [data.nextstrain.org/files/workflows/dengue/metadata_denv4.tsv.zst](https://data.nextstrain.org/files/workflows/dengue/metadata_denv4.tsv.zst) -For more information about the dengue lineage system, to submit questions, or lineage proposals; please visit [dengue-lineages.org](https://dengue-lineages.org/). \ No newline at end of file + +### Lineage coloring + +There are up to six different lineage coloring options available depending on the source of data: + +**Based on a Nextclade call against [community/v-gen-lab/dengue datasets](https://github.com/nextstrain/nextclade_data/tree/master/data/community/v-gen-lab/dengue).** + +The lineage color options are split into levels of detail, with an example shown beside each level: + +* **Genotype (Nextclade):** 3III +* **Major Lineage (Nextclade):** 3III_B +* **Minor Lineage (Nextclade):** 3III_B.3.2 + +For more information about the dengue lineage system please visit [dengue-lineages.org](https://dengue-lineages.org/). + +**Based on NCBI GenBank metadata** + +* **Serotype (GenBank metadata):** denv1 to denv4 + +**Based on Augur clade assignment (`clade_membership`)** +_(Only available for genome trees, not gene trees)_ +* **Serotype (Nextstrain):** DENV1 – DENV4, annotated only on the "all" tree +* **Genotype (Nextstrain):** such as DENV3/III _(equivalent to 3III in "Genotype (Nextclade)")_, annotated only on the serotype-specific trees.