Transition Priors for Protein Hidden Markov Models: An Empirical Study towards Maximum Discrimination. - Markus Wistrand; Erik L. L. Sonnhammer (J. Comput. Biol., 2004)

Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER. - Markus Wistrand; Erik L. L. Sonnhammer (BMC Bioinform., 2005)