Numerical recipes in C (2nd ed.): the art of scientific computing
Numerical recipes in C (2nd ed.): the art of scientific computing
DNA sequence evolution with neighbor-dependent mutation
Proceedings of the sixth annual international conference on Computational biology
A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology
Two Methods for Improving Performance of a HMM and their Application for Gene Finding
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology
RECOMB '03 Proceedings of the seventh annual international conference on Research in computational molecular biology
Computational identification of evolutionarily conserved exons
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Identifying Conserved Discriminative Motifs
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
Graphical Models, Exponential Families, and Variational Inference
Foundations and Trends® in Machine Learning
Variational upper bounds for probabilistic phylogenetic models
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
New Methods for Inference of Local Tree Topologies with Recombinant SNP Sequences in Populations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site to the next. These models combine phylogenetic models of molecular evolution, which apply to individual sites, and hidden Markov models, which allow for changes from site to site. Besides improving the realism of ordinary phylogenetic models, they are potentially very powerful tools for inference and prediction---for gene finding, for example, or prediction of secondary structure. In this paper, we review progress on combined phylogenetic and hidden Markov models and present some extensions to previous work. Our main result is a simple and efficient method for accommodating higher-order states in the HMM, which allows for context-sensitive models of substitution---that is, models that consider the effects of neighboring bases on the pattern of substitution. We present experimental results indicating that higher-order states, autocorrelated rates, and multiple functional categories all lead to significant improvements in the fit of a combined phylogenetic and hidden Markov model, with the effect of higher-order states being particularly pronounced.