Due to small probabilities for long protein sequences numerical
underflow errors are occurring.

Log transform has been implemented in the viterbi algorithm. The viterbi
algorithm is used in place of the ap_viterbi algorithm. This is also
true for the parameter init in the _clustering() function. The
DEF.big_negative and DEF.big_positive const values have been updated by
a few orders of magnitude.

(1) Test different input representations
	--> msa profile (created)
	--> hydrophobic moment profile (created)
	--> msa + hyydrophobic moment profiles (created)
	--> pca of msa profile (need to create)
	--> single seq + msa profile (created)

(2) PSICOV --> contact map estimation
	--> look for significant local correlation as most people only search
		for non-local correlation for beta-strands
	--> data stored on server at /gluster/data/tmb_maps.tgz
	
(3) Non-negative matrix factorisation or Principle Component Analysis
	for input encoding dimension reduction

(4) Different grammars, mixtures, and window sizes
	--> tied at mixture level not state level
	--> different mixture numbers (1,3,and 4)
	--> window sizes (7,15,19,21,31)