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.