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Set state-based clock rate based on literature search
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From May et al, 2011 "Phylogeography of West Nile Virus: From the Cradle of Evolution in Africa to Eurasia, Australia, and the Americas"
https://journals.asm.org/doi/10.1128/jvi.01963-10

Table 1, IS98-STD and North America 6.53E-04
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j23414 committed Nov 1, 2024
1 parent 0354f12 commit bf0ed7c
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion phylogenetic/build-configs/washington-state/config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ subsampling:
force_include: --exclude-all --include ../nextclade/defaults/include.txt

refine:
treetime_params: --coalescent opt --clock-filter-iqd 4 --date-inference marginal --date-confidence
treetime_params: --coalescent opt --clock-filter-iqd 4 --date-inference marginal --date-confidence --clock-rate 0.000653

traits:
metadata_columns: [
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