augur clades
Assign clades to nodes in a tree based on amino-acid or nucleotide signatures.
usage: augur clades [-h] [--tree TREE] [--mutations MUTATIONS [MUTATIONS ...]]
[--reference REFERENCE [REFERENCE ...]] [--clades CLADES]
[--output-node-data OUTPUT_NODE_DATA]
Named Arguments
- --tree
prebuilt Newick – no tree will be built if provided
- --mutations
JSON(s) containing ancestral and tip nucleotide and/or amino-acid mutations
- --reference
fasta files containing reference and tip nucleotide and/or amino-acid sequences
- --clades
TSV file containing clade definitions by amino-acid
- --output-node-data
name of JSON file to save clade assignments to