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