% ./taxit -h


usage: taxit [-h] [-V]

             {info,rollback,help,create,strip,taxids,new_database,check,reroot,refpkg_intersection,lonelynodes,update_taxids,rp,add_nodes,rollforward,update,findcompany,taxtable}
             ...

Creation, validation, and modification of reference packages for use with
`pplacer` and related software.

positional arguments:
  {info,rollback,help,create,strip,taxids,new_database,check,reroot,refpkg_intersection,lonelynodes,update_taxids,rp,add_nodes,rollforward,update,findcompany,taxtable}
    help                Detailed help for actions using `help <action>`
    add_nodes           Add new nodes to a database containing a taxonomy.
    check               Run a series of deeper checks on a RefPkg.
    create              Creates a reference package
    findcompany         Find company for lonely nodes.
    info                Show information about reference packages.
    lonelynodes         Extracts tax ids of all lonely nodes in a taxtable.
    new_database        Create a database containing an entire taxonomy
    refpkg_intersection
                        Find the intersection of a taxtable and a refpkg's
                        taxonomy.
    reroot              Taxonomically reroots a reference package
    rollback            Rollback a refpkg to undo the previous command.
    rollforward         Rollforward a rolled back command on a refpkg.
    rp                  Resolve path; get the path to a file in the reference
                        package.
    strip               Removes all rollback and rollforward information and
                        files not attached to the current state from a refpkg.
    taxids              Look up a set of tax_ids from taxonomic names
    taxtable            Creates a CSV file describing lineages for a set of
                        taxa
    update              Adds or updates files or metdata in a refpkg.
    update_taxids       Update obsolete tax_ids in preparation for use in
                        taxtable. Takes sequence info

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         Print the version number and exit