====== MS4: Multi Scale Selector of Sequence Signatures ======

Download the latest version {{:logiciels:ms4_beta-0.2.tar.gz|here}}.


This   implementation   t_MS4  is   a   beta   release   of  the   MS4
algorithm. t_MS4 uses previous  development : NLD-decoding to find NLD
classes (C part of the code, included) and [[http://pypi.python.org/pypi/altgraph/|altgraph]] to manage trees. It requires [[http://www.python.org/|Python 2]].\\



MS4 is a method that selects among all the segments of similarity detected 
by the N-local decoding algorithm (Didier //et al.//, 2007) those on which 
a classification of unaligned set of sequences is based. The N-local decoding 
detects local similarity of size 2N-1 containing a variable number of 
mismatch and it has been proved to be successful for alignment-free 
classification for fixed value of N. The aim of this method is to 
automatically adapt N  (the size of the similarities  detected) to the
local context and the data-set under consideration. Then, it  computes a 
dissimilarity  matrix   based  on  these   detected  similarities  for
classifying sequences. For low values of N, similarities are spurious 
and  many  hits occur  inside  one sequence. For  large  values of  N, 
similarities are exact words shared by no more than 2 sequences. 
MS4 fixes N  as the average number of  occurrences per sequence that
are smaller than a given parameter Kappa ([[http://www.biomedcentral.com/1471-2105/11/406 |Corel et al., 2010]]).