mdust new implementation of the DUST module that uses the same function to assign a complexity score to a sequence, but uses a different rule by which high-scoring sequences are masked.

Usage:

mdust [<fasta-file>] [-w <wsize>] [-v <cut-off>] [-m N|X|L] [-c]
  if no <fasta-file> is given, a multi-fasta stream is expected at stdin
  -v default <cut-off> value is 28 (lower values might mask more,
  but possibly still useful sequence; > 64 will rarely mask poly-triplets)
  -w set maximum word size to <wsize> (default 3)
  -m if fasta output is not disabled by -c, set the masking letter type:
     N ('N', default), X ('X'), L (make lowercase)
  -c output masking coordinates only:
     seq_name, seqlength, mask_start, mask_end  (tab delimited)

Reference:

A fast and symmetric DUST implementation to mask low-complexity DNA sequences.
Morgulis A, Gertz EM, Schäffer AA, Agarwala R.
J Comput Biol. 2006 Jun;13(5):1028-40.
PMID:16796549