.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH RPPR "1" "June 2020" "rppr 1.1~alpha19" "User Commands"
.SH NAME
rppr \- tool for working with reference packages
.SH SYNOPSIS
.B rppr
<command> [options]
.SH OPTIONS
.SS "available commands"
.TP
check
checks a reference package
.TP
convex_taxids
determines convex tax_ids per\-rank in a refpkg
.TP
convexify
identifies minimal leaf set to cut for taxonomic concordance
.TP
infer
infers classifications of unclassified sequences in a reference package
.TP
info
gives information about a reference package
.TP
min_adcl
finds a good collection of sequences to cut from a placefile's ref tree
.TP
min_adcl_tree
finds a good collection of sequences to cut from a tree
.TP
pdprune
prunes the tree to maximize PD
.TP
prep_db
makes SQL enabling taxonomic querying of placement results
.TP
prepsim
makes a simulation by taking out taxids and turning them into fake placements
.TP
reclass
reclassifies nonconvex sequences in a reference package
.TP
ref_tree
writes a taxonomically annotated reference tree and an induced taxonomic tree
.TP
reroot
reroots a given reference package in place
.PP
To get more help about a given command, type rppr COMMAND \fB\-\-help\fR
.SS "Additional options"
.TP
\fB\-\-version\fR
Print version and exit
.TP
\fB\-\-cmds\fR
Print a list of the available commands.
.TP
\fB\-\-batch\fR
Run the provided batch file of guppy commands
.TP
\fB\-\-quiet\fR
Don't write messages to stdout (unless explicitly requested).
.TP
\fB\-\-help\fR
Display this list of options and subcommands
.TP
\fB\-help\fR
Display this list of options and subcommands
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.