NAME

       rppr - tool for working with reference packages

SYNOPSIS

       rppr <command> [options]

OPTIONS

   available commands
       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 --help

   Additional options
       --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

AUTHOR

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