[Biojava-l] Problem with SingleDP.viterbi(..)

[Stephan Neumann]

Hello,

we have a question concerning the Viterbi algorithm in BioJava:
We are building Profile HMMs and performing BaumWelch algorithm to
improve them. Finally we are performing the Viterbi algorithm on the
resulting dynamic programming matrix (SingleDP). Now, we are wondering
where is the difference between the different ScoreTypes: (ODDS,
PROBABILITY, NULL_MODEL) of SingleDP.viterbi and how can we interpret
the resulting StatePaths. Furthermore, what does StatePath.getScore mean?

Best regards,
Stephan.