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feat: replace Python variables with pathvars
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feat: replace Python variables with pathvars
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feat: replace Python variables with pathvars
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fix dataset pathvar in param
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revert CONTEXT_FASTA to null
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update .gitignore
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fix: ensure formatted results include only selected samples
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fix: apply negative branch length correction iteratively (#45)
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fix: apply negative branch length correction iteratively (#45)
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fix: apply negative tree branch length correction iteratively
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fix: apply negative branch length correction while there are negative…
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build: update index_fasta environment
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refactor: require FASTA index as input for all-sites VCF
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