Hidden paralogy check

Check for hidden paralogy in gene trees

Command identity

Canonical command:

hidden_paralogy_check

Handler:

hidden_paralogy_check

Aliases:

clan_check

Standalone executables:

pk_hidden_paralogy_check, pk_clan_check

Categories:

Homology assessment

Runtime interface

Synopsis

phykit hidden_paralogy_check <tree> [--clade <clade>] [--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
-c, --clade	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

Scan tree for evidence of hidden paralogy.

This analysis can be used to identify hidden paralogy. Specifically, this method will examine if a set of well known monophyletic taxa are, in fact, monophyletic. If they are not, the evolutionary history of the gene may be subject to hidden paralogy. This analysis is typically done with single-copy orthologous genes.

Requires a clade file, which specifies which monophyletic lineages to check for. Multiple monophyletic lineages can be specified. Each lineage should be specified on a single line and each tip name (or taxon name) should be separated by a space. For example, if it is anticipated that tips "A", "B", and "C" are monophyletic and "D", "E", and "F" are expected to be monophyletic, the clade file should be formatted as follows:
"
A B C
D E F
"

The output will report if the specified taxa were monophyletic or not. The number of rows will reflect how many groups of taxa were checked for monophyly. For example, if there were three rows of clades in the -c file, there will be three rows in the output where the first row in the output corresponds to the results of the first row in the clade file.

The concept behind this analysis follows Siu-Ting et al., Molecular Biology and Evolution (2019), doi: 10.1093/molbev/msz067.

phykit hidden_paralogy_check <tree> -c/--clade <clade_file> [--json]

Options:
-t/--tree: input file tree name
-c/--clade: clade file detailing which monophyletic lineages should be scanned for
--json: optional argument to print results as JSON