Authors:Erick Matsen and Aaron Gallagher
License:GPL v3
Date:September 2011

rppr is a binary to help prepare reference packages and select sequences. It’s pronounced “ripper” and is short for Reference Package PReparer. “Evaluator” might be a more appropriate descriptor than “preparer”, but acronym aesthetics won out over precision here.


Command line interface

The general way to invoke rppr is rppr COMMAND [options] placefile[s] where COMMAND is one of the rppr commands. For example:

rppr info -c some.refpkg

These programs are listed with more detail below, and can always be found using rppr --cmds .

rppr can also be invoked as rppr --quiet COMMAND [...], which prevents the specified command from writing to stdout unless explicitly requested.

List of subcommands

The following table provides links to more in-depth documentation for each rppr subcommand:

Command Description
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