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]
                    [--validation-mode {error,warn,skip}] [--skip-validation]

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

--clades

TSV file containing clade definitions by amino-acid

--output-node-data

name of JSON file to save clade assignments to

--membership-name

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

Default: 'clade_membership'

--label-name

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

Default: 'clade'

--validation-mode

Possible choices: error, warn, skip

Control if optional validation checks are performed and what happens if they fail.

‘error’ and ‘warn’ modes perform validation and emit messages about failed validation checks. ‘error’ mode causes a non-zero exit status if any validation checks failed, while ‘warn’ does not.

‘skip’ mode performs no validation.

Note that some validation checks are non-optional and as such are not affected by this setting.

Default: error

--skip-validation

Skip validation of input/output files, equivalent to –validation-mode=skip. Use at your own risk!