rppr - tool for working with reference packages

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

rppr 1.1~alpha19                                    June 2020                                            RPPR(1)

       rppr - tool for working with reference packages

availablecommands
       check  checks a reference package

       convex_taxids
              determines convex tax_ids per-rank in a refpkg

       convexify
              identifies minimal leaf set to cut for taxonomic concordance

       infer  infers classifications of unclassified sequences in a reference package

       info   gives information about a reference package

       min_adcl
              finds a good collection of sequences to cut from a placefile's ref tree

       min_adcl_tree
              finds a good collection of sequences to cut from a tree

       pdprune
              prunes the tree to maximize PD

       prep_db
              makes SQL enabling taxonomic querying of placement results

       prepsim
              makes a simulation by taking out taxids and turning them into fake placements

       reclass
              reclassifies nonconvex sequences in a reference package

       ref_tree
              writes a taxonomically annotated reference tree and an induced taxonomic tree

       reroot reroots a given reference package in place

       To get more help about a given command, type rppr COMMAND --helpAdditionaloptions--version
              Print version and exit

       --cmds Print a list of the available commands.

       --batch
              Run the provided batch file of guppy commands

       --quiet
              Don't write messages to stdout (unless explicitly requested).

       --help Display this list of options and subcommands

       -help  Display this list of options and subcommands

rppr <command> [options]