.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXMRCACUT "1" "July 2021" "pxmrcacut 1.3" "User Commands"
.SH NAME
pxmrcacut \- manual page for pxmrcacut 1.3
.SH SYNOPSIS
.B pxmrcacut
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
Extract subclade(s) from tree(s).
This will take a newick\- or nexus\-formatted tree from a file or STDIN,
and an MRCA file with format:
MRCANAME = tip1 tip2 ...
If multiple MRCAs are provided, multiple subtrees are returned
.SH OPTIONS
.TP
\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
input newick tree file, STDIN otherwise
.TP
\fB\-m\fR, \fB\-\-mrca\fR=\fI\,FILE\/\fR
file containing MRCA declarations
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output newick 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 2013\-2021 FePhyFoFum
License GPLv3