.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH PROK-GENESEEK "1" "March 2017" "prok-geneseek 1.2.12" "User Commands"
.SH NAME
prok-geneseek \- <optional description of the program>
.SH SYNOPSIS
.B prok-geneseek
[\fI\,options\/\fR] \fI\,<database> <sequences \/\fR...\fI\,>\/\fR
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-S\fR START, \fB\-\-start\fR=\fI\,START\/\fR
define a start codon [default: \fB\-S\fR ATG]
.TP
\fB\-E\fR STOP, \fB\-\-stop\fR=\fI\,STOP\/\fR
define a stop codon [default: \fB\-E\fR TAG \fB\-E\fR TAA \fB\-E\fR TGA]
.TP
\fB\-j\fR THREADS, \fB\-\-threads\fR=\fI\,THREADS\/\fR
number of threads [default: 16]
.TP
\fB\-p\fR PROCESSES, \fB\-\-processes\fR=\fI\,PROCESSES\/\fR
number of parallel processes to run [default: 2]
.TP
\fB\-e\fR EVALUE, \fB\-\-evalue\fR=\fI\,EVALUE\/\fR
maximum e\-value [default: 1e\-30]
.TP
\fB\-I\fR IDENTITY, \fB\-\-identity\fR=\fI\,IDENTITY\/\fR
minimum percent identity [default: 0.45]
.TP
\fB\-L\fR FRACTION, \fB\-\-length\fR=\fI\,FRACTION\/\fR
allowable relative error in hit length [default: 0.2]
.TP
\fB\-O\fR bases, \fB\-\-orflen\fR=\fI\,bases\/\fR
minimum allowable length for ORFs [default: 300]
.TP
\fB\-d\fR DIRECTORY, \fB\-\-directory\fR=\fI\,DIRECTORY\/\fR
set working directory [default: current]
.TP
\fB\-P\fR PLOTTER, \fB\-\-plotter\fR=\fI\,PLOTTER\/\fR
plotting module [default: biotools.analysis.plot]
.TP
\fB\-v\fR, \fB\-\-verbose\fR
print debug messages [default: False]
.TP
\fB\-\-no\-plots\fR
suppress the drawing of plots [default: False]
.TP
\fB\-\-no\-predict\fR
don't predict genes, instead treat the input files as
predicted genes [default: False]
.TP
\fB\-\-no\-cluster\fR
don't cluster the sequences, instead treat the input
files as alignments [default: False]
.TP
\fB\-\-no\-rename\fR
don't rename the fasta and clustal files [default:
False]
.TP
\fB\-\-no\-reports\fR
don't generate files for variance data [default:
False]
.TP
\fB\-\-no\-calculation\fR
don't calculate sequence variance [default: False]
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.