[Biojava-l] odds ratio

[wendy wong]

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