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


Script to generate an artificial reference genome (AR) from a given input. The AR fullfills 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

-h, --help

show this help message and exit

-d DISTANCE, --distance=DISTANCE

distance between 2 mutations on DNA level. The minimum distance will then be d-3. [default: 15]

-o ORF, --orf=ORF

1- protect ORF structure from mutations. 0 - allow mutations in start / stop codon [default: 1]

-r REVSUB, --revsub=REVSUB

1 - reverse substitution if no suitable counterpart was found (balanced mutation). 0 - keep the unbalanced mutations.[default: 1]

-m RANDOM, --random=RANDOM

1/0 variable. 1 - shuffled starting positions for the

  • mutations. 0 - linear mutation [default: 1]

-s SORF, --saveorfs=SORF

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: ]

-l LORF, --loadorfs=LORF

Specify filename to a previously created pickle file (contains positions of start/stop codons) [default: ]

-n NAME, --name=NAME

Specify name which will be used as header. [default: ]


set to 1 if you want to print examples