Co-evolution Is Incompatible With the Markov Assumption in Phylogenetics

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Statistics Papers
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Markov processes
biological techniques
biology computing
genetics
microorganisms
molecular biophysics
Markov assumption
Markov models
fungi
phylogenetics
probabilistic models
computational biology
co-evolution
models of molecular evolution
phylogenetic reconstruction
animals
evolution
molecular
humans
Markov chains
phylogeny
proteins
Biology
Biostatistics
Computer Sciences
Genetics and Genomics
Statistics and Probability
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Tuller, Tamir
Mossel, Elchanan
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Abstract

Markov models are extensively used in the analysis of molecular evolution. A recent line of research suggests that pairs of proteins with functional and physical interactions co-evolve with each other. Here, by analyzing hundreds of orthologous sets of three fungi and their co-evolutionary relations, we demonstrate that co-evolutionary assumption may violate the Markov assumption. Our results encourage developing alternative probabilistic models for the cases of extreme co-evolution.

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2011-11-01
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IEEE/ACM Transactions on Computational Biology and Bioinformatics
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