---
name: "rppr"
section: "1"
platform: "linux"
package: "pplacer"
version: "1.1~alpha19-4"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/rppr"
---

# rppr(1)

tool for working with reference packages

## 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.