.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXRECODE "1" "July 2021" "pxrecode 1.3" "User Commands"
.SH NAME
pxrecode \- manual page for pxrecode 1.3
.SH SYNOPSIS
.B pxrecode
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
Nucleotide sequence recoding.
This will take fasta, fastq, phylip, and nexus formats from a file or STDIN.
.SH OPTIONS
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
input sequence file, STDIN otherwise
.TP
\fB\-r\fR, \fB\-\-recode\fR=\fI\,STRING\/\fR
string identifying recoding scheme (default: RY)
.IP
Supported recodings (use any valid combination):
.IP
R = A|G
Y = C|T
S = C|G
W = A|T
M = A|C
K = G|T
B = C|G|T
D = A|G|T
H = A|C|T
V = A|C|G
.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 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