.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXRLS "1" "July 2021" "pxrls 1.3" "User Commands"
.SH NAME
pxrls \- manual page for pxrls 1.3
.SH SYNOPSIS
.B pxrls
[\fI\,OPTIONS\/\fR]... \fI\,FILES\/\fR
.SH DESCRIPTION
Taxon relabelling for alignments.
This will take fasta, phylip, and nexus formats from a file or STDIN.
Two ordered lists of taxa, \fB\-c\fR (current) and \fB\-n\fR (new) must be provided.
Results are written in fasta format.
.SH OPTIONS
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
input seq file, STDIN otherwise
.TP
\fB\-c\fR, \fB\-\-cnames\fR=\fI\,FILE\/\fR
file containing current taxon labels (one per line)
.TP
\fB\-n\fR, \fB\-\-nnames\fR=\fI\,FILE\/\fR
file containing new taxon labels (one per line)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
make the output more verbose
.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 Joseph W. Brown, 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 2016\-2021 FePhyFoFum
License GPLv3