.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH PSORT "1" "April 2017" "psort 3.0.4" "User Commands"
.SH NAME
psort \- bacterial localization prediction tool
.SH SYNOPSIS
.B psort
[\fI\,-p|-n\/\fR] [\fI\,OPTIONS\/\fR] [\fI\,SEQFILE\/\fR]
.SH DESCRIPTION
Runs psort on the sequence file SEQFILE .  If SEQFILE isn't provided
then sequences will be read from STDIN.
.TP
\fB\-\-help\fR, \fB\-h\fR
Displays usage information
.TP
\fB\-\-positive\fR, \fB\-p\fR
Gram positive bacteria
.TP
\fB\-\-negative\fR, \fB\-n\fR
Gram negative bacteria
.TP
\fB\-\-archaea\fR, \fB\-a\fR
Archaea
.TP
\fB\-\-cutoff\fR, \fB\-c\fR
Sets a cutoff value for reported results
.TP
\fB\-\-divergent\fR, \fB\-d\fR
Sets a cutoff value for the multiple
localization flag
.TP
\fB\-\-matrix\fR, \fB\-m\fR
Specifies the path to the pftools installation.  If
not set, defaults to the value of the PSORT_PFTOOLS
environment variable.
.TP
\fB\-\-format\fR, \fB\-f\fR
Specifies sequence format (default is FASTA)
.TP
\fB\-\-exact\fR, \fB\-e\fR
Skip SCLBLASTe (useful for batch runs of data
against itself in SCLBLAST)
.TP
\fB\-\-output\fR, \fB\-o\fR
Specifies the format for the output (default is
\&'normal'  Value can be one of: terse, long or normal
.TP
\fB\-\-root\fR, \fB\-r\fR
Specify PSORT_ROOT for running local copies.  If
not set, defaults to the value of the PSORT_ROOT
environment variable.
.TP
\fB\-\-server\fR, \fB\-s\fR
Specifies the PSort server to use
.TP
\fB\-\-verbose\fR, \fB\-v\fR
Be verbose while running
.HP
\fB\-\-x\-skip\-localization\fR
.TP
\fB\-\-version\fR
Print the version of PSortb
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.