Subtree pruning and regrafting

Generate all SPR rearrangements for a specified subtree

Command identity

Canonical command:

subtree_prune_regraft

Handler:

subtree_prune_regraft

Aliases:

spr

Standalone executables:

pk_subtree_prune_regraft, pk_spr

Categories:

Tree manipulation & utilities

Runtime interface

Synopsis

phykit subtree_prune_regraft --tree <tree> --subtree <subtree> [--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
-t, --tree	true	str	required	any
--subtree	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

Generate all possible SPR (Subtree Pruning and Regrafting) rearrangements for a specified subtree on a tree.

The subtree is identified by specifying one or more comma-separated taxa whose MRCA (most recent common ancestor) defines the clade to prune. The pruned subtree is then regrafted onto every other branch in the remaining tree, producing one Newick tree per regraft position.

For a subtree defined by a single taxon (a single leaf), the leaf is pruned and reattached to each branch in the remaining tree. For a clade (two or more taxa), the entire clade is pruned and regrafted. Each output Newick contains all original taxa.

phykit subtree_prune_regraft -t <tree> --subtree <taxa> [-o/--output <output_file>] [--json]

Options:
-t/--tree: input tree file in Newick format (required)
--subtree: comma-separated list of taxa defining the subtree to prune (MRCA resolved), or a single-column file with one taxon per line (required)
-o/--output: optional output file for SPR trees (one Newick per line); if omitted, prints to stdout
--json: optional argument to print summary metadata and trees as JSON