Alignment subsampling

Randomly subsample genes, partitions, or sites

Command identity

Canonical command:: alignment_subsample
Handler:: alignment_subsample
Aliases:: aln_subsample, subsample
Standalone executables:: pk_alignment_subsample, pk_aln_subsample, pk_subsample
Categories:: Alignment & dataset utilities

Runtime interface

Synopsis

phykit alignment_subsample --mode <mode> [--alignment <alignment>] [--list <list>] [--partition <partition>] [--number <number>] [--fraction <fraction>] [--seed <seed>] [--bootstrap] [--output <output>] [--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
`--mode`	true	str	required	genes, partitions, sites
`-a, --alignment`	false	str	none	any
`-l, --list`	false	str	none	any
`-p, --partition`	false	str	none	any
`--number`	false	int	none	any
`--fraction`	false	float	none	any
`--seed`	false	int	none	any
`--bootstrap`	false	boolean	false	any
`-o, --output`	false	str	subsampled	any
`--json`	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Output-file options: --output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Randomly subsample genes, partitions, or sites from phylogenomic datasets. Supports three modes:

genes: Given a file listing alignment paths, randomly select N of them.
partitions: Given a supermatrix + RAxML-style partition file, randomly select N partitions and extract their columns into a new alignment.
sites: Given a single alignment, randomly select N columns.

Sampling can be without replacement (default, for jackknife-style tests) or with replacement using --bootstrap (for gene/site bootstrapping). Use --seed for reproducibility.

# Subsample 50 genes from a list of 200
phykit alignment_subsample --mode genes -l gene_list.txt --number 50 -o sub50

# Subsample 50% of partitions from a supermatrix
phykit alignment_subsample --mode partitions -a concat.fa -p concat.partition \
    --fraction 0.5 --seed 42 -o sub50pct

# Bootstrap-resample sites from an alignment
phykit alignment_subsample --mode sites -a alignment.fa \
    --number 500 --bootstrap --seed 1 -o boot1

Options:
--mode: subsampling mode: genes, partitions, or sites (required)
-a/--alignment: input alignment file in FASTA format (required for partitions and sites modes)
-l/--list: file listing alignment paths, one per line (required for genes mode)
-p/--partition: RAxML-style partition file (required for partitions mode)
--number: exact number of items to select (mutually exclusive with --fraction)
--fraction: fraction of items to select, 0.0 to 1.0 (mutually exclusive with --number)
--bootstrap: sample with replacement (default: without replacement)
--seed: random seed for reproducibility
-o/--output: output file prefix (default: subsampled)
--json: optional argument to print results as JSON