NAME¶

SYNOPSIS¶

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¶