>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?
Sounds correct. >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? If you used an odds scoring function then you have done things correctly. Sounds wierd. - Mark _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
