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