.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH PXCAT "1" "July 2021" "pxcat 1.3" "User Commands"
.SH NAME
pxcat \- manual page for pxcat 1.3
.SH SYNOPSIS
.B pxcat
[\fI\,OPTIONS\/\fR]... \fI\,FILES\/\fR
.SH DESCRIPTION
Sequence file concatenation.
Can use wildcards e.g.:
.IP
pxcat \fB\-s\fR *.phy \fB\-o\fR my_cat_file.fa
.SS "However, if the argument list is too long (shell limit), put filenames in a file:"
.IP
for x in *.phy
.IP
do echo $x >> flist.txt
.IP
done
.SS "and call using the -f option:"
.IP
pxcat \fB\-f\fR flist.txt \fB\-o\fR my_cat_file.fa
.PP
This will take fasta, fastq, phylip, and nexus sequence formats.
Individual files may be of different formats.
.SH OPTIONS
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
list of input sequence files (space delimited)
.TP
\fB\-f\fR, \fB\-\-flistFILE\fR
file listing input files (one per line)
.TP
\fB\-p\fR, \fB\-\-partf\fR=\fI\,FILE\/\fR
output partition file, none otherwise
.TP
\fB\-u\fR, \fB\-\-uppercase\fR
export characters in uppercase
.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 F. Walker, 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 2015\-2021 FePhyFoFum
License GPLv3