NAME

       tantan - low complexity and tandem repeat masker for biosequences

SYNOPSIS

       tantan [options] fasta-sequence-file(s)

DESCRIPTION

       Find simple repeats in sequences

   Options (default settings):
       -p     interpret the sequences as proteins

       -x     letter to use for masking, instead of lowercase

       -c     preserve uppercase/lowercase in non-masked regions

       -m     file for letter pair scores (+1/-1, but -p selects BLOSUM62)

       -r     probability of a repeat starting per position (0.005)

       -e     probability of a repeat ending per position (0.05)

       -w     maximum tandem repeat period to consider (100, but -p selects 50)

       -d     probability decay per period (0.9)

       -a     gap existence cost (0)

       -b     gap extension cost (infinite: no gaps)

       -s     minimum repeat probability for masking (0.5)

       -f     output type: 0=masked sequence, 1=repeat probabilities,

              2=repeat counts, 3=BED (0)

       -h, --help
              show help message, then exit

       --version
              show version information, then exit

REPORTING BUGS

       Report bugs to: tantan@cbrc.jp
       Home page: http://www.cbrc.jp/tantan/