Treeness over RCV

Treeness over relative composition variability

Command identity

Canonical command:

treeness_over_rcv

Handler:

treeness_over_rcv

Aliases:

tor, toverr

Standalone executables:

pk_treeness_over_rcv, pk_tor, pk_toverr

Categories:

Saturation & model adequacy

Runtime interface

Synopsis

phykit treeness_over_rcv --alignment <alignment> --tree <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
-a, --alignment	true	str	required	any
-t, --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/RCV for a given alignment and tree.

Higher treeness/RCV values are thought to be desirable because they indicate a high signal-to-noise ratio and suggest the data are least susceptible to composition bias.

PhyKIT reports three tab delimited values: col1: treeness/RCV col2: treeness col3: RCV

Calculate treeness/RCV following Phillips and Penny, Molecular Phylogenetics and Evolution (2003), doi: 10.1016/S1055-7903(03)00057-5.

phykit treeness_over_rcv -a/--alignment <alignment> -t/--tree <tree> [--json]

Options:
-a/--alignment: an alignment file
-t/--tree: a tree file
--json: optional argument to print results as JSON