Mask alignment

Mask sites in an alignment

Command identity

Canonical command:

mask_alignment

Handler:

mask_alignment

Aliases:

mask, mask_aln

Standalone executables:

pk_mask_alignment, pk_mask, pk_mask_aln

Categories:

Alignment & dataset utilities

Runtime interface

Synopsis

phykit mask_alignment <alignment> [--max_gap <max_gap>] [--min_occupancy <min_occupancy>] [--max_entropy <max_entropy>] [--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
-g, --max_gap	false	float	1.0	any
-o, --min_occupancy	false	float	0.0	any
-e, --max_entropy	false	float	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

Mask alignment sites based on threshold criteria.

Sites are retained when they pass all active thresholds: maximum gap fraction, minimum occupancy, and maximum site entropy.

phykit mask_alignment <alignment> [-g/--max_gap <float>] [-o/--min_occupancy <float>] [-e/--max_entropy <float>] [--json]

Options:
<alignment>: first argument after function name should be an alignment file
-g/--max_gap: maximum allowed fraction of missing/invalid characters at a site (default: 1.0)
-o/--min_occupancy: minimum required occupancy at a site (default: 0.0)
-e/--max_entropy: maximum allowed site entropy (default: no filter)
--json: optional argument to print results as JSON