Degree of violation of the molecular clock

Measure molecular clock violation

Command identity

Canonical command:

degree_of_violation_of_a_molecular_clock

Handler:

dvmc

Aliases:

dvmc

Standalone executables:

pk_degree_of_violation_of_a_molecular_clock, pk_dvmc

Categories:

Tree summary statistics

Runtime interface

Synopsis

phykit degree_of_violation_of_a_molecular_clock <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 degree of violation of a molecular clock (or DVMC) in a phylogeny.

Lower DVMC values are thought to be desirable because they are indicative of a lower degree of violation in the molecular clock assumption.

Typically, outgroup taxa are not included in molecular clock analysis. Thus, prior to calculating DVMC from a single gene tree, users may want to prune outgroup taxa from the phylogeny. To prune tips from a phylogeny, see the prune_tree function.

Calculate DVMC in a tree following Liu et al., PNAS (2017), doi: 10.1073/pnas.1616744114.

phykit degree_of_violation_of_a_molecular_clock <tree> [--json]

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