Occupancy per taxon

Taxon occupancy in alignment columns

Command identity

Canonical command:

occupancy_per_taxon

Handler:

occupancy_per_taxon

Aliases:

occ_tax, occupancy_taxon

Standalone executables:

pk_occupancy_per_taxon, pk_occ_tax, pk_occupancy_taxon

Categories:

Alignment quality & statistics

Runtime interface

Synopsis

phykit occupancy_per_taxon <alignment> [--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
alignment	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

Calculate occupancy per taxon in an alignment.

Occupancy is the fraction of valid (non-gap/non-ambiguous) characters for each taxon.

phykit occupancy_per_taxon <alignment> [--json]

Example output:

1       0.8333
2       0.6667

Options:
<alignment>: first argument after function name should be an alignment file
--json: optional argument to print results as JSON