.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXBP "1" "July 2021" "pxbp 1.3" "User Commands"
.SH NAME
pxbp \- manual page for pxbp 1.3
.SH SYNOPSIS
.B pxbp
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
This will print out bipartitions found in treefile.
Trees are assumed rooted unless the \fB\-e\fR argument is provided.
This will take a newick\- or nexus\-formatted tree from a file or STDIN.
.SH OPTIONS
.TP
\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
input treefile, STDIN otherwise
.TP
\fB\-v\fR, \fB\-\-verbose\fR
give more output
.TP
\fB\-e\fR, \fB\-\-edgeall\fR
force edgewise (not node \- so when things are unrooted) and
assume all taxa are present in all trees
.TP
\fB\-u\fR, \fB\-\-uniquetree\fR
output unique trees and *no* other output
.TP
\fB\-m\fR, \fB\-\-maptree\fR=\fI\,FILE\/\fR
put the bipart freq on the edges of this tree. This will
create a *.pxbpmapped.tre file.
.TP
\fB\-c\fR, \fB\-\-cutoff\fR
skip biparts that have support lower than this.
.TP
\fB\-s\fR, \fB\-\-suppress\fR
don't print all the output (maybe you use this
with the maptree feature
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output 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)
.SH "REPORTING BUGS"
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
.SH COPYRIGHT
Copyright \(co 2017\-2021 FePhyFoFum
License GPLv3