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Add E gene trees#18

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j23414 wants to merge 14 commits intomainnextstrain/dengue:mainfrom phylogenetic_dir_Enextstrain/dengue:phylogenetic_dir_ECopy head branch name to clipboard

+246-53

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Commits on May 2, 2024

• Copy newreference script from RSV

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• Prepare E sequences for phylogenetic analysis

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• Construct phylogeny for E gene

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• Generate node data for E gene trees

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• Export E gene builds

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• Include root sequences in E build

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• Update snakemake targets

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• Use wildcards and combine redundant rules

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• Use wildcards conditionals to further combine rules

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• Consistent naming of reference genome files

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• Rename rule to describe what it does instead of the internal tool it uses.

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• Exclude outliers

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• AWS cores

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Commits on May 6, 2024

• fixup: denv2 reference genbank

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