Hi, I am trying to set up an HMM wth a few states. I have a background state with background distribution. For the rest of the states, I set up the distribution and then use the setNullModel to set the null distribution to the background distribution. Am I doing the right thing?
The reason why I am asking is when I tried using the forward backward algorithm, the scores of the state that I am interested in at each site is greater than 2000. I would expect some sites to have a number less than 1 to indicate that it is more likely to be in the null distribution, or am I doing something totally wrong here? thanks, wendy _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
