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