.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXRR "1" "July 2021" "pxrr 1.3" "User Commands"
.SH NAME
pxrr \- manual page for pxrr 1.3
.SH SYNOPSIS
.B pxrr
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
Reroot (or unroot) a tree file and produce a newick.
This will take a newick\- or nexus\-formatted tree from a file or STDIN.
Output is written in newick format.
.SH OPTIONS
.TP
\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
input tree file, STDIN otherwise
.TP
\fB\-g\fR, \fB\-\-outgroups\fR=\fI\,CSL\/\fR
outgroup sep by commas (NO SPACES!)
.TP
\fB\-f\fR, \fB\-\-namesf\fR=\fI\,FILE\/\fR
outgroups in a file (each on a line)
.TP
\fB\-r\fR, \fB\-\-ranked\fR
turn on ordering of outgroups. will root on first one present
.TP
\fB\-u\fR, \fB\-\-unroot\fR
unroot the tree
.TP
\fB\-s\fR, \fB\-\-silent\fR
do not error if outgroup(s) not found
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output tree file, STOUT otherwise
.TP
\fB\-h\fR, \fB\-\-help\fR
display this help and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
display version and exit
.TP
\fB\-C\fR, \fB\-\-citation\fR
display phyx citation and exit
.SH CITATION
Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.
.SH AUTHOR
Written by Stephen A. Smith (blackrim), Joseph W. Brown
.SH "REPORTING BUGS"
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
.SH COPYRIGHT
Copyright \(co 2014\-2021 FePhyFoFum
License GPLv3