NAME

       gt-seqmutate - Mutate the sequences of the given sequence file(s).

SYNOPSIS

       gt seqmutate [option ...] [sequence_file ...]

OPTIONS

       -rate
           set the mutation rate (default: 1)

       -width
           set output width for FASTA sequence printing (0 disables formatting) (default: 0)

       -o
           redirect output to specified file (default: undefined)

       -gzip
           write gzip compressed output file (default: no)

       -bzip2
           write bzip2 compressed output file (default: no)

       -force
           force writing to output file (default: no)

       -help
           display help and exit

       -version
           display version information and exit

DESCRIPTION

       For each position in the given sequences it is randomly determined with probability (mutation rate / 100)
       if the given position is mutated. If so, in 80% of the cases a substitution is performed, in 10% an
       insertion, and in 10% a deletion, respectively. For substitution and insertion events, the nucleotide i s
       generated randomly without regard to the original nucleotide. That is, resubstitutions are possible. This
       procedure equals the one described on page 1867 of the following paper

       T.D. Wu and C.K. Watanabe. GMAP: a genomic mapping and alignment program for mRNA and EST sequences.
       Bioinformatics, 21(9):1859-1875, 2005.

AUTHOR

       Report bugs to <gt-users@genometools.org>.

                                                   10/07/2012                                    GT-SEQMUTATE(1)