Bug#815672: ITP: spaced -- alignment-free sequence comparison using spaced words

[Fabian Kl?tzl <kloetzl@evolbio.mpg.de>]

Package: wnpp
Severity: wishlist
Owner: Debian Med Team <debian-med@lists.debian.org>

* Package name    : spaced
  Version         : 1.0.2
  Upstream Author : Lars Hahn <lars.hahn@stud.uni-goettingen.de>
* URL             : http://spaced.gobics.de/
* License         : GPL
  Programming Lang: C++
  Description     : 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.

This package will be maintained by the DebianMed Team.