Mpox lineage in metadata is different from what shows in the tree

General
1

We’re using a fork from the mpox repo 2 years ago and I just wanted to check in case there is an obvious answer for this.

We have some samples that have lineage B.1.20 in the metadata (downloaded from data.nextstrain.org/files/workflows/mpox/metadata.tsv.gz)

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But are showing up as B.1 on the tree

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I dug around and vaguely remember something about the color_ordering.tsv needs to have all lineages we want to show on the tree. Is that right?

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In any case, what is the best approach to make sure all lineages show up in the tree? Any pointers would be appreciated!

2

The lineages on the tree are assigned using the clades.tsv file in your fork from 2 years ago:

The clades in the metadata use a recent nextclade dataset which includes additional lineages that were defined in the mean time.

you have two options:

  • update the clades.tsv to a more version
  • color the tree by metadata without using the phylogenetic clade determination step in the workflow.

does that make sense?

3

All makes sense. I’ll look into it. Thanks very much!