.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.1.
.TH PXCONTRATES "1" "July 2023" "pxcontrates 1.3" "User Commands"
.SH NAME
pxcontrates \- continuous character rate estimation with Brownian and OU
.SH SYNOPSIS
.B pxcontrates
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
Continuous character rate estimation with Brownian and OU.
This will take fasta, phylip, and nexus formats from a file or STDIN.
.SH OPTIONS
.TP
\fB\-c\fR, \fB\-\-charf\fR=\fI\,FILE\/\fR
input character file, STDIN otherwise
.TP
\fB\-t\fR, \fB\-\-treef\fR=\fI\,FILE\/\fR
input tree file, STDIN otherwise
.TP
\fB\-a\fR, \fB\-\-analysis\fR=\fI\,NUM\/\fR
analysis type (0=anc[DEFAULT], 1=ratetest)
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output sequence 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 2013\-2021 FePhyFoFum
License GPLv3