Parsimony score

Fitch parsimony score of a tree given an alignment

Command identity

Canonical command:

parsimony_score

Handler:

parsimony_score

Aliases:

pars, parsimony

Standalone executables:

pk_parsimony_score, pk_pars, pk_parsimony

Categories:

Trait evolution

Runtime interface

Synopsis

phykit parsimony_score --tree <tree> --alignment <alignment> [--verbose] [--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
-a, --alignment	true	str	required	any
-v, --verbose	false	boolean	false	any
--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

Compute the Fitch (1971) maximum parsimony score of a tree given an alignment. The parsimony score is the minimum number of character state changes required to explain the alignment on the given tree topology. Gap characters (-, N, X, ?) are treated as wildcards.

Cross-validated against R's phangorn::parsimony(method="fitch").

phykit parsimony_score -t <tree> -a <alignment> [-v/--verbose] [--json]

Options:
-t/--tree: tree file (required)
-a/--alignment: alignment file in FASTA format (required)
-v/--verbose: print per-site parsimony scores
--json: optional argument to print results as JSON

R validation: Validated against phangorn in R (see tests/r_validation/validate_parsimony.R).