From 24ce6dd85bdeadc24a59616e382a08a16a5ac9d3 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 13 Jan 2025 11:38:39 -0800
Subject: [PATCH] Link to lineage designation repo

This should be useful for users to understand how lineages used in the
dataset are defined.
---
 phylogenetic/defaults/description.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/phylogenetic/defaults/description.md b/phylogenetic/defaults/description.md
index 29ae51f..840b673 100644
--- a/phylogenetic/defaults/description.md
+++ b/phylogenetic/defaults/description.md
@@ -16,7 +16,7 @@ Our bioinformatic processing workflow can be found at [github.com/nextstrain/mpo
 - masking several regions of the genome, including the first 1350 and last 6422 base pairs and multiple repetitive regions of variable length
 - phylogenetic reconstruction using [IQTREE-2](http://www.iqtree.org/)
 - ancestral state reconstruction and temporal inference using [TreeTime](https://github.com/neherlab/treetime)
-- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/-/phylogenetic/defaults/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc...
+- clade assignment via [clade definitions defined here](https://github.com/nextstrain/mpox/blob/-/phylogenetic/defaults/clades.tsv), to label broader MPXV clades I, IIa and IIb and to label hMPXV1 lineages A, A.1, A.1.1, etc. (defined by [mpxv-lineages/lineage-designation](https://github.com/mpxv-lineages/lineage-designation))
 
 #### Underlying data
 We curate sequence data and metadata from the [NCBI Datasets command line tools](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/),