Class ClusterReduction

Specialization for ReducedAminoAcid

/*!
 * @class ClusterReduction
 * 
 * @headerfile seqan/reduced_aminoacid.h
 * 
 * @brief Specialization for @link ReducedAminoAcid @endlink
 * 
 * @signature template <unsigned char n, unsigned char m = 24, typename TMatrix
 *            = Blosum62> struct ClusterReduction;
 * 
 * @tparam n the size of the reduced alphabet (between 2 and m-1)
 * @tparam m size to truncate alphabet to, <b>before</b> clustering (one of 20,
 *           22, 24; default 24)
 * @tparam TMatrix Matrix used for clustering (default @link Blosum62 @endlink,
 *                 none other supported right now)
 * 
 * @section WhenToUse
 * 
 * Use m = 24 when you expect 'X' and '*' in the dataset you reduce from. This
 * is especially the case on translated genomic reads.
 * 
 * If you have validated protein sequences, you can use can use m = 20 or m =
 * 22, which will not include special characters (see @link AminoAcid @endlink
 * for details).
 * 
 * @section Background
 * 
 * The method employed for reducing the alphabet is similar to Murphy et al,
 * 2000, <a href="http://www.ncbi.nlm.nih.gov/pubmed/10775656">http://www.ncbi.n
 * lm.nih.gov/pubmed/10775656</a>
 * 
 * Correlation coefficients for the Blosum62 scores of all pairs of amino acids
 * in the alphabet were computed and clustered with WPGMA (using UPGMA as second
 * criterium when WPGMA yields the same distance between two clusters).
 * 
 * <img src="ClusterReduction.png">
 * 
 * The exact clustering for m = 24.
 */