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. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
