Evolutionary rate

Calculate tree-based evolutionary rate

Command identity

Canonical command:

evolutionary_rate

Handler:

evolutionary_rate

Aliases:

evo_rate

Standalone executables:

pk_evolutionary_rate, pk_evo_rate

Categories:

Tree summary statistics

Runtime interface

Synopsis

phykit evolutionary_rate <tree> [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
tree	true	str	required	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Unless the guidance below states otherwise, results are emitted as command output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Calculate a tree-based estimation of the evolutionary rate of a gene.

Evolutionary rate is the total tree length divided by the number of terminals.

Calculate evolutionary rate following Telford et al., Proceedings of the Royal Society B (2014).

phykit evolutionary_rate <tree> [--json]

Options:
<tree>: input file tree name
--json: optional argument to print results as JSON