Last common ancestor subtree

Extract subtree from LCA of specified taxa

Command identity

Canonical command:

last_common_ancestor_subtree

Handler:

last_common_ancestor_subtree

Aliases:

lca_subtree

Standalone executables:

pk_last_common_ancestor_subtree, pk_lca_subtree

Categories:

Tree manipulation & utilities

Runtime interface

Synopsis

phykit last_common_ancestor_subtree <tree> <list_of_taxa> [--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
list_of_taxa	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

Obtains subtree from a phylogeny by getting the last common ancestor from a list of taxa.

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

Options:
<tree>: first argument after function name should be a tree file
<list_of_taxa>: second argument after function name should be a single column file with the list of taxa to get the last common ancestor subtree for
-o/--output: optional argument to name the outputted tree file
--json: optional argument to print results as JSON