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Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics
November/December 2011 (vol. 8 no. 6)
pp. 1667-1670
Tamir Tuller, Weizmann Institute of Science, Rehovot
Elchanan Mossel, Weizmann Institute of Science, Rehovot and University of California Berkeley, Berkeley
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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Index Terms:
Markov models, models of molecular evolution, co-evolution, phylogenetic reconstruction.
Tamir Tuller, Elchanan Mossel, "Co-evolution Is Incompatible with the Markov Assumption in Phylogenetics," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 6, pp. 1667-1670, Nov.-Dec. 2011, doi:10.1109/TCBB.2010.124
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