Long branch score

Identify long branches in a tree

Command identity

Canonical command:

long_branch_score

Handler:

lb_score

Aliases:

lb_score, lbs

Standalone executables:

pk_long_branch_score, pk_lb_score, pk_lbs

Categories:

Tree summary statistics

Runtime interface

Synopsis

phykit long_branch_score <tree> [--verbose] [--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
-v, --verbose	false	boolean	false	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 long branch (LB) scores in a phylogeny.

Lower LB scores are thought to be desirable because they are indicative of taxa or trees that likely do not have issues with long branch attraction.

LB score is the mean pairwise patristic distance of taxon i compared to all other taxa divided by the average pairwise patristic distance.

PhyKIT reports summary statistics. To obtain LB scores for each taxon, use the -v/--verbose option.

LB scores are calculated following Struck, Evolutionary Bioinformatics (2014), doi: 10.4137/EBO.S14239.

phykit long_branch_score <tree> [-v/--verbose] [--json]

Options:
<tree>: first argument after function name should be a tree file
-v/--verbose: optional argument to print all LB score values
--json: optional argument to print results as JSON