.TH RNR-PRUNE "1" "March 2017" "rnr-prune 1.0" "User Commands"
.SH NAME
rnr-prune \- prunes a list of taxa from a bootstrap tree or a single tree with branch lengths
.SH SYNOPSIS
.B rnr\-prune
[\-i <bootTrees> | \fB\-t\fR <treeFile>] \fB\-x\fR <excludeFile> \fB\-n\fR <runId> [\-w <workingDir>] [\-h]
.SH DESCRIPTION
This program prunes a list of taxa from a bootstrap tree or a single tree with branch lengths (such as a best\-known ML/MP\-tree).
.SH OPTIONS
.SS OBLIGATORY
.TP
\fB\-x\fR <excludeFile>
A list of taxa (one taxon per line) to prune from either the bootstrap trees or the single best\-known tree.
.TP
\fB\-i\fR <bootTrees>
A collection of bootstrap trees.
.TP
\fB\-t\fR <treeFile>
A single tree with branch lengths. Use either this flag or the \fB\-i\fR flag.
.TP
\fB\-n\fR <runId>
An identifier for this run.
.SS OPTIONAL
.TP
\fB\-w\fR <workDir>
A working directory where output files are created.
.TP
\fB\-h\fR
This help file.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.