Internode labeler

Label internal nodes of a tree

Command identity

Canonical command:

internode_labeler

Handler:

internode_labeler

Aliases:

il

Standalone executables:

pk_internode_labeler, pk_il

Categories:

Tree manipulation & utilities

Runtime interface

Synopsis

phykit internode_labeler <tree> [--output <output>] [--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
-o, --output	false	str	none	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Output-file options: --output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Appends numerical identifiers to bipartitions in place of support values. This is helpful for pointing to specific internodes in supplementary files or otherwise.

phykit internode_labeler <tree> [-o/--output <file>] [--json]

Options:
<tree>: first argument after function name should be a tree file
-o/--output: optional argument to name the outputted tree file
--json: optional argument to print results as JSON