Root tree

Root or reroot a tree

Command identity

Canonical command:

root_tree

Handler:

root_tree

Aliases:

root, rt

Standalone executables:

pk_root_tree, pk_root, pk_rt

Categories:

Tree manipulation & utilities

Runtime interface

Synopsis

phykit root_tree <tree> --root <root> [--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
-r, --root	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

Roots phylogeny using user-specified taxa.

A list of taxa to root the phylogeny on should be specified using the -r argument. The root_taxa file should be a single-column file with taxa names. The output file will have the same name as the input tree file but with the suffix ".rooted".

phykit root_tree <tree> -r/--root <root_taxa> [-o/--output <output_file>] [--json]

Options:
<tree>: first argument after function name should be a tree file to root
-r/--root: single column file with taxa names to root the phylogeny on
-o/--output: optional argument to specify the name of the output file
--json: optional argument to print results as JSON