.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.1.
.TH PXNW "1" "July 2023" "pxnw 1.3" "User Commands"
.SH NAME
pxnw \- conduct Needleman\-Wunsch analysis for all the seqs in a file
.SH SYNOPSIS
.B pxnw
[\fI\,OPTIONS\/\fR]...
.SH DESCRIPTION
Conduct Needleman\-Wunsch analysis for all the seqs in a file.
This will take fasta, fastq, phylip, and nexus formats from a file or STDIN.
Output is a list of the scores and distances (and the alignments if asked).
.SH OPTIONS
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
input sequence file, STDIN otherwise
.TP
\fB\-a\fR, \fB\-\-outalnf\fR=\fI\,FILE\/\fR
output sequence file, won't output otherwise
.TP
\fB\-t\fR, \fB\-\-seqtype\fR=\fI\,INT\/\fR
sequence type, default=DNA (DNA=0,AA=1)
.TP
\fB\-m\fR, \fB\-\-matrix\fR=\fI\,FILE\/\fR
scoring matrix, default DNA=EDNAFULL, AA=BLOSUM62
.TP
\fB\-n\fR, \fB\-\-nthreads\fR=\fI\,INT\/\fR
number of threads (open mp), default=2
.TP
\fB\-v\fR, \fB\-\-verbose\fR
make the output more verbose, turns off parallel
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output score/distance 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