Consensus tree

Consensus tree from multiple trees

Command identity

Canonical command:

consensus_tree

Handler:

consensus_tree

Aliases:

consensus, ctree

Standalone executables:

pk_consensus_tree, pk_consensus, pk_ctree

Categories:

Tree comparison & consensus

Runtime interface

Synopsis

phykit consensus_tree --trees <trees> [--method <method>] [--missing-taxa <missing_taxa>] [--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, --trees	true	str	required	any
-m, --method	false	str	majority	strict, majority
--missing-taxa	false	str	error	error, shared
--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

Infer a consensus tree from a collection of trees.

Input can be either: 1) a file with one Newick tree per line, or 2) a file with one tree-file path per line.

Consensus methods: * majority: majority-rule consensus (default)
* strict: strict consensus

Missing taxa handling: * --missing-taxa error (default): exits if trees do not share identical tip sets
* --missing-taxa shared: prunes all trees to the intersection of taxa before inferring consensus

phykit consensus_tree -t/--trees <trees> [-m/--method strict|majority] [--missing-taxa error|shared] [--json]

Options:
-t/--trees: file containing trees (one Newick per line) or tree-file paths (one per line)
-m/--method: consensus method (strict or majority; default: majority)
--missing-taxa: handling strategy for mismatched taxa (error or shared; default: error)
--json: optional argument to print results as JSON