.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH PXNJ "1" "June 2021" "pxnj 1.2" "User Commands"
.SH NAME
pxnj \- manual page for pxnj 1.2
.SH SYNOPSIS
.B pxnj
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
Basic neighbour\-joining tree maker.
This will take fasta, fastq, phylip, and nexus inputs from a file or STDIN.
.SH OPTIONS
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
input sequence file, STDIN otherwise
.TP
\fB\-n\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
number of threads, default=1
.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 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