.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH PXSW "1" "May 2018" "pxsw 0.99+ds" "User Commands"
.SH NAME
pxsw \- Conduct Smith-Waterman analysis for all the seqs in a file.
.SH SYNOPSIS
.B pxsw
[\fI\,OPTION\/\fR]... [\fI\,FILE\/\fR]...
.SH DESCRIPTION
Conduct Smith\-Waterman analysis for all the seqs in a file.
This will take fasta, fastq, phylip, and nexus inputs.
Output is a list of the scores and distances (and the alignments
if asked).
Can read from stdin or file.
.TP
\fB\-s\fR, \fB\-\-seqf\fR=\fI\,FILE\/\fR
input sequence file, stdin otherwise
.TP
\fB\-o\fR, \fB\-\-outf\fR=\fI\,FILE\/\fR
output score/distance file, stout 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\-h\fR, \fB\-\-help\fR
display this help and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
display version and exit
.SH "REPORTING BUGS"
Report bugs to: <https://github.com/FePhyFoFum/phyx/issues>
phyx home page: <https://github.com/FePhyFoFum/phyx>
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.