DOKK / manpages / debian 12 / arden / arden-create.1.en

arden-create - generate an artificial reference genome (AR) from a given input

arden-create [options] [OUTPUTFOLDER] [INPUT FASTA]...

Script to generate an artificial reference genome (AR) from a given input. The AR fulfills the following conditions by default settings:

has a nucleotide distribution equal to the input genome
has an amino acid (aa) distribution equal to the input genome
keeps the aa neighborhood similar to the neighborhood in input genome
protects start and stop codons from mutations

Required Arguments:

complete path to output destination folder
Single sequence Fasta file.
show program's version number and exit
show this help message and exit
distance between 2 mutations on DNA level. The minimum distance will then be d-3. [default: 15]
1- protect ORF structure from mutations. 0 - allow mutations in start / stop codon [default: 1]
1 - reverse substitution if no suitable counterpart was found (balanced mutation). 0 - keep the unbalanced mutations.[default: 1]
1/0 variable. 1 - shuffled starting positions for the
mutations. 0 - linear mutation [default: 1]
Save found start and stop codons in a pickle file (can be loaded if the input fasta is used again if a filename is specified). [default: ]
Specify filename to a previously created pickle file (contains positions of start/stop codons) [default: ]
Specify name which will be used as header. [default: ]
set to 1 if you want to print examples
February 2014 arden-create 2013-04-25