Polytomy testing

Test for polytomies in a tree

Command identity

Canonical command:

polytomy_test

Handler:

polytomy_test

Aliases:

polyt, polyt_test, ptt

Standalone executables:

pk_polytomy_test, pk_polyt, pk_polyt_test, pk_ptt

Categories:

Tree comparison & consensus

Runtime interface

Synopsis

phykit polytomy_test [--trees <trees>] [--groups <groups>] [--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	false	str	none	any
-g, --groups	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

Conduct a polytomy test for three clades in a phylogeny.

Polytomy tests can be used to identify putative radiations as well as identify well supported alternative topologies.

The polytomy testing function takes as input a file with the three groups of taxa to test the relationships for and a single column file with the names of the desired tree files to use for polytomy testing. Next, the script examines support for the grouping of the three taxa using triplets and gene support frequencies.

This function can account for uncertainty in gene trees - that is, the input phylogenies can have collapsed bipartitions.

Thereafter, a chi-squared test is conducted to determine if there is evidence to reject the null hypothesis wherein the null hypothesis is that the three possible topologies among the three groups are equally supported. This test is done using gene support frequencies.

phykit polytomy_test -t/--trees <trees> -g/--groups <groups> [--json]

Options:
-t/--trees <trees>: single column file with the names of phylogenies to use for polytomy testing
-g/--groups: a tab-delimited file with the grouping designations to test. Lines starting with comments are not considered. Names of individual taxa should be separated by a semi-colon ';'
--json: optional argument to print results as JSON

For example, the groups file could look like the following:

#label group0  group1  group2
name_of_test    tip_name_A;tip_name_B   tip_name_C  tip_name_D;tip_name_E