Robinson-Foulds distance

Topological distance between trees

Command identity

Canonical command:

robinson_foulds_distance

Handler:

rf_distance

Aliases:

rf, rf_dist, rf_distance

Standalone executables:

pk_robinson_foulds_distance, pk_rf, pk_rf_dist, pk_rf_distance

Categories:

Tree comparison & consensus

Runtime interface

Synopsis

phykit robinson_foulds_distance <tree_zero> <tree_one> [--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_zero	true	str	required	any
tree_one	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 Robinson-Foulds (RF) distance between two trees.

Low RF distances reflect greater similarity between two phylogenies. This function prints out two values, the plain RF value and the normalized RF value, which are separated by a tab. Normalized RF values are calculated by taking the plain RF value and dividing it by 2(n-3) where n is the number of tips in the phylogeny. Prior to calculating an RF value, PhyKIT will first determine the number of shared tips between the two input phylogenies and prune them to a common set of tips. Thus, users can input trees with different topologies and infer an RF value among subtrees with shared tips.

PhyKIT will print out col 1: the plain RF distance and col 2: the normalized RF distance.

RF distances are calculated following Robinson & Foulds, Mathematical Biosciences (1981), doi: 10.1016/0025-5564(81)90043-2.

phykit robinson_foulds_distance <tree_file_zero> <tree_file_one> [--json]

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