Treeness

Ratio of internal to total branch lengths

Command identity

Canonical command:: treeness
Handler:: treeness
Aliases:: tness
Standalone executables:: pk_treeness, pk_tness
Categories:: Tree summary statistics

Runtime interface

Synopsis

phykit treeness <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 treeness statistic for a phylogeny.

Higher treeness values are thought to be desirable because they represent a higher signal-to-noise ratio.

Treeness is the sum of internal branch lengths divided by the total tree length. Therefore, values range from 0 to 1. Treeness can be used as a measure of the signal-to-noise ratio in a phylogeny.

Calculate treeness (also referred to as stemminess) following Lanyon, The Auk (1988), doi: 10.1093/auk/105.3.565 and Phillips and Penny, Molecular Phylogenetics and Evolution (2003), doi: 10.1016/S1055-7903(03)00057-5.

phykit treeness <tree> [--json]

Options:
<tree>: first argument after function name should be a tree file
--json: optional argument to print results as JSON