augur clades

Assign clades to nodes in a tree based on amino-acid or nucleotide signatures.

Nodes which are members of a clade are stored via <OUTPUT_NODE_DATA> → nodes → <node_name> → clade_membership and if this file is used in augur export v2 these will automatically become a coloring.

The basal nodes of each clade are also given a branch label which is stored via <OUTPUT_NODE_DATA> → branches → <node_name> → labels → clade.

The keys “clade_membership” and “clade” are customisable via command line arguments.

usage: augur clades [-h] --tree TREE --mutations NODE_DATA_JSON
                    [NODE_DATA_JSON ...] --clades TSV
                    [--output-node-data NODE_DATA_JSON]
                    [--membership-name MEMBERSHIP_NAME]
                    [--label-name LABEL_NAME]

Named Arguments


prebuilt Newick – no tree will be built if provided


JSON(s) containing ancestral and tip nucleotide and/or amino-acid mutations


TSV file containing clade definitions by amino-acid


name of JSON file to save clade assignments to


Key to store clade membership under; use “None” to not export this

Default: “clade_membership”


Key to store clade labels under; use “None” to not export this

Default: “clade”