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Pseudoknots in RNA secondary structures., and . RECOMB, page 201-209. ACM, (2000)RNA Secondary Structure Prediction by Minimum Free Energy.. Encyclopedia of Algorithms, Springer, (2008)StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees., , , and . Bioinformatics, 24 (20): 2403-2404 (2008)Fast evaluation of internal loops in RNA secondary structure prediction., , and . Bioinformatics, 15 (6): 440-445 (1999)The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search., , and . Nucleic Acids Research, 33 (Web-Server-Issue): 650-653 (2005)RNA Pseudoknot Prediction in Energy-Based Models., and . Journal of Computational Biology, 7 (3-4): 409-427 (2000)Solving the String Statistics Problem in Time O(n log n)., , , and . ICALP, volume 2380 of Lecture Notes in Computer Science, page 728-739. Springer, (2002)Complexity of Comparing Hidden Markov Models., and . ISAAC, volume 2223 of Lecture Notes in Computer Science, page 416-428. Springer, (2001)RNA Secondary Structure Prediction Including Pseudoknots.. Encyclopedia of Algorithms, Springer, (2008)Comparing a Hidden Markov Model and a Stochastic Context-Free Grammar., , and . WABI, volume 2149 of Lecture Notes in Computer Science, page 69-94. Springer, (2001)