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    ToPS: a framework to manipulate probabilistic models of sequence data. by André Yoshiaki Kashiwabara, Igor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Mitchell Durham

    Published 2013-01-01
    “…We present ToPS, a computational framework that can be used to implement different applications in bioinformatics analysis by combining eight kinds of models: (i) independent and identically distributed process; (ii) variable-length Markov chain; (iii) inhomogeneous Markov chain; (iv) hidden Markov model; (v) profile hidden Markov model; (vi) pair hidden Markov model; (vii) generalized hidden Markov model; and (viii) similarity based sequence weighting. …”
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