Swap from list of force included strains to list of excluded strains #38
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In the genome build, we had force included the entire cattle clade. In this commit, I swap to force including a few particular strains (like the human case) and instead make an exclude list of 2024 strains from North America that group outside the cattle clade.
trvrb
commented
May 22, 2024
jameshadfield
approved these changes
May 23, 2024
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I ran this locally and it works as expected. A few of the sequences are moving around the tree a lot as they have a bunch of mutations pulling them in different directions. LHS in my rebuild vs your rebuild from this branch on the RHS:
For example, A/dairycattle/Texas/24009308001/2024 has 3 homoplasies which mean it sometimes jumps to a different position (where it would then have a different set of homoplasies):
As noted in slack, the commercial milk / environmental sample needs a host update in Fauna.
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In the genome build, we had force included the entire cattle clade. In this commit, I swap to force including a few particular strains (like the human case) and instead make an exclude list of 2024 strains from North America that group outside the cattle clade.
The resulting tree is visible at https://nextstrain.org/staging/avian-flu/h5n1-cattle-outbreak/genome