taxon_list

List available taxonomic-specific marker sets.

Produces a table indicating all taxa for which a taxonomic-specific marker set can be produced with the taxon_set command. Use --rank to restrict the list to a taxonomic rank (e.g., life, domain, phylum, …).

Arguments

usage: checkm taxon_list [-h] [--rank {ALL,life,domain,phylum,class,order,family,genus,species}]
                         [--tmpdir TMPDIR]

List available taxonomic-specific marker sets.

options:
  -h, --help            show this help message and exit
  --rank {ALL,life,domain,phylum,class,order,family,genus,species}
                        restrict list to specified taxonomic rank (default: ALL)
  --tmpdir TMPDIR       specify an alternative directory for temporary files

Example: checkm taxon_list --rank phylum

Example

checkm taxon_list
checkm taxon_list --rank phylum