Patristic distances

Pairwise patristic distances between taxa

Command identity

Canonical command:

patristic_distances

Handler:

patristic_distances

Aliases:

pd

Standalone executables:

pk_patristic_distances, pk_pd

Categories:

Tree summary statistics

Runtime interface

Synopsis

phykit patristic_distances <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 summary statistics among patristic distances in a phylogeny.

Patristic distances are all tip-to-tip distances in a phylogeny.

To obtain all patristic distances, use the -v/--verbose option. With the -v option, the first column will have two taxon names separated by a '-' followed by the patristic distance. Features will be tab separated.

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

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