prok-geneseek - <optional description of the program>
prok-geneseek [options] <database>
<sequences ...>
- -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]
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.