dishonest_comp

#Comparison of Dishonest Casino Models in R-HMM, Mamot, HMMoc, and StochHMM.

##Mamot Dishonest Casino Model

# HMM for the "dishonest casino" presented by Durbin, Eddy, Krogh, Mitchison 
# in "Biological sequence analysis" (Cambridge University Press, 1998).
# Exercise 1.1, p. 6 and p. 54, 56, 59, 61, 65

Alphabet: abcdef
################################################
State BEGIN
	E: 0  0  0  0  0  0
	T: F 1
# Fair
State F
	E: 0.1666  0.1666  0.1666  0.1666  0.1666  0.1666
	T: F 0.95  L 0.049  END 0.001
# not fair
State L 
	E: 0.1 0.1 0.1 0.1 0.1 0.5
	T: F 0.1  L 0.9
State END  
	E: 0  0  0  0  0  0
	T: END 0
################################################
NULLMODEL:  0.1666  0.1666  0.1666  0.1666  0.1666  0.1666