alignment-free sequence comparison using spaced words

 Spaced (Words) is a new approach to alignment-free sequence
 comparison. While most alignment-free algorithms compare the
 word-composition of sequences, spaced uses a pattern of care and
 don't care positions. The occurrence of a spaced word in a sequence
 is then defined by the characters at the match positions only, while
 the characters at the don't care positions are ignored. Instead of
 comparing the frequencies of contiguous words in the input sequences,
 this new approach compares the frequencies of the spaced words according
 to the pre-defined pattern. An information-theoretic distance measure
 is then used to define pairwise distances on the set of input sequences
 based on their spaced-word frequencies. Systematic test runs on real and
 simulated sequence sets have shown that, for phylogeny reconstruction,
 this multiple-spaced-words approach is far superior to the classical
 alignment-free approach based on contiguous word frequencies.