Monophyly check

Test monophyly of a group of taxa

Command identity

Canonical command:

monophyly_check

Handler:

monophyly_check

Aliases:

is_monophyletic

Standalone executables:

pk_monophyly_check, pk_is_monophyletic

Categories:

Tree manipulation & utilities

Runtime interface

Synopsis

phykit monophyly_check <tree> <list_of_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
tree	true	str	required	any
list_of_taxa	true	str	required	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

This analysis can be used to determine if a set of taxa are exclusively monophyletic. By exclusively monophyletic, if other taxa are in the same clade, the lineage will not be considered exclusively monophyletic.

Requires a taxa file, which specifies which tip names are expected to be monophyletic. File format is a single column file with tip names. Tip names not present in the tree will not be considered when examining monophyly.

The output will have six columns. col 1: if the clade was or wasn't monophyletic col 2: average bipartition support value in the clade of interest col 3: maximum bipartition support value in the clade of interest col 4: minimum bipartition support value in the clade of interest col 5: standard deviation of bipartition support values in the clade of interest col 6: tip names of taxa monophyletic with the lineage of interest excluding those that are listed in the taxa_of_interest file

phykit monophyly_check <tree> <list_of_taxa> [--json]

Options:
<tree>: first argument after function name should be a tree file
<list_of_taxa>: single column file with list of tip names to examine the monophyly of
--json: optional argument to print results as JSON