The script flags the mRNAs containing premature stop codons. It will add the attribute "pseudo" and the value will be the positions of all premature stop codons. Gene are flagged as pseudogene only if all the isoforms are pseudogenes. The attribute will also be "pseudo" but will not contains any location.

SYNOPSIS --gff infile.gff --fasta infile.fa --out outfile --help


  • --gff, --ref or -reffile

    Input GTF/GFF file.

  • -f, --fa or --fasta

    Imput fasta file.

  • --ct, --codon or --table

    Codon table to use. [default 1]

  • --out, --output or -o

    Output gff3 file where the result will be printed.

  • --help or -h

    Display this helpful text.