From df0308937aa60337bdfa58aa94fe2d84a9db35c9 Mon Sep 17 00:00:00 2001 From: Trevor Bedford Date: Fri, 23 Aug 2024 14:18:36 -0700 Subject: [PATCH] Update clade definition and coloring This commit: 1. Very slightly changes clade definition for "clade II". This results in no change to the resulting clade assignments. Previously clade II definitions included nucleotide positions 35253 and 150970. However, neither of these positions show variation: - nextstrain.org/mpox/all-clades?c=gt-nuc_35253 - nextstrain.org/mpox/all-clades?c=gt-nuc_150970 I updated these sites to 20605 and 174146 which show variation between clades I and II. 2. The color ordering lacked entries for clade Ia and clade Ib. This resulted in gray colors for these two clades at nextstrain.org/mpox/all-clades. --- phylogenetic/defaults/clades.tsv | 4 ++-- phylogenetic/defaults/color_ordering.tsv | 3 ++- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/phylogenetic/defaults/clades.tsv b/phylogenetic/defaults/clades.tsv index a8a5c3f..11857c9 100644 --- a/phylogenetic/defaults/clades.tsv +++ b/phylogenetic/defaults/clades.tsv @@ -11,9 +11,9 @@ clade Ia nuc 35352 A clade Ib clade clade I clade Ib nuc 19455 T +clade II nuc 20605 A clade II nuc 86502 G -clade II nuc 150970 A -clade II nuc 35352 C +clade II nuc 174146 C clade IIa clade clade II clade IIa nuc 54013 G diff --git a/phylogenetic/defaults/color_ordering.tsv b/phylogenetic/defaults/color_ordering.tsv index 2be351e..5e61aa9 100644 --- a/phylogenetic/defaults/color_ordering.tsv +++ b/phylogenetic/defaults/color_ordering.tsv @@ -16884,7 +16884,8 @@ recency New ################ - +clade_membership Ia +clade_membership Ib clade_membership I clade_membership II clade_membership IIa