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Use gene reference files to generate E gene trees #48

Merged
merged 8 commits into from
May 13, 2024
Merged

Use gene reference files to generate E gene trees #48

merged 8 commits into from
May 13, 2024

Commits on May 10, 2024

  1. prepare sequences

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  2. annotate phylogeny

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    j23414 committed May 10, 2024
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  3. Add E gene targets

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    j23414 committed May 10, 2024
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  4. Set E tree default color to Nextclade genotype

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  5. fixup: denv2 genotype ordering to match clade_membership

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    j23414 committed May 10, 2024
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  6. E gene builds exclude the augur clades call 

    Until we have a set of E gene serotype and genotype defining mutations,
skip the augur clades call for E gene builds. This was originally discussed
for commit:

2f48ddb

Used in measles:

nextstrain/measles@ab92a1b

And diagrammed in:

#17 (comment)
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    j23414 committed May 10, 2024
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  7. Add NCBI serotypes annotations to the phylogeny 

    Add ncbi_serotype annotation to phylogeny, since this can be used as a
source-of-truth when adding E gene defining serotypes in subsequent PRs.
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    j23414 committed May 10, 2024
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Commits on May 11, 2024

  1. fixup: change default display to rooted time-tree 

    Mirroring the change from measles commit:

* nextstrain/measles@862dbaf
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    j23414 committed May 11, 2024
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