Bipartition support statistics

Summary statistics of bipartition support values

Command identity

Canonical command:: bipartition_support_stats
Handler:: bipartition_support_stats
Aliases:: bss
Standalone executables:: pk_bipartition_support_stats, pk_bss
Categories:: Tree summary statistics

Runtime interface

Synopsis

phykit bipartition_support_stats <tree> [--verbose] [--thresholds <thresholds>] [--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
`-v, --verbose`	false	boolean	false	any
`--thresholds`	false	str	none	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

Calculate summary statistics for bipartition support.

High bipartition support values are thought to be desirable because they are indicative of greater certainty in tree topology.

To obtain all bipartition support values, use the -v/--verbose option. In addition to support values for each node, the names of all terminal branch tips are also included. Each terminal branch name is separated with a semi-colon (;).

phykit bipartition_support_stats <tree> [-v/--verbose]
    [--thresholds <comma-separated-floats>] [--json]

Options:
<tree>: first argument after function name should be a tree file
-v/--verbose: optional argument to print all bipartition support values
--thresholds: optional comma-separated support cutoffs; prints count and fraction of bipartitions below each cutoff
--json: optional argument to print results as JSON

Example JSON output (summary mode):

phykit bipartition_support_stats test.tre --thresholds 70,90 --json
{"summary": {"maximum": 100, "mean": 95.71428571428571, "median": 100, "minimum": 85, "seventy_fifth": 100.0, "standard_deviation": 7.319250547113999, "twenty_fifth": 92.5, "variance": 53.57142857142857}, "thresholds": [{"count_below": 0, "fraction_below": 0.0, "threshold": 70.0}, {"count_below": 2, "fraction_below": 0.2857142857142857, "threshold": 90.0}], "verbose": false}

Example JSON output (verbose mode):

phykit bipartition_support_stats test.tre -v --json
{"bipartitions": [{"support": 85, "terminals": ["taxon_a", "taxon_b"]}, {"support": 100, "terminals": ["taxon_c", "taxon_d"]}], "thresholds": [], "verbose": true}