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Gain-loss-duplication models for copy number evolution on a phylogeny: Exact algorithms for computing the likelihood and its gradient

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  • Csűrös, Miklós

Abstract

Gene gain-loss-duplication models are commonly based on continuous-time birth–death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes. While the applications are becoming more varied and demanding, bioinformatics methods for probabilistic inference on copy numbers (or integer-valued evolutionary characters, in general) are scarce.

Suggested Citation

  • Csűrös, Miklós, 2022. "Gain-loss-duplication models for copy number evolution on a phylogeny: Exact algorithms for computing the likelihood and its gradient," Theoretical Population Biology, Elsevier, vol. 145(C), pages 80-94.
    • Handle: RePEc:eee:thpobi:v:145:y:2022:i:c:p:80-94
    DOI: 10.1016/j.tpb.2022.03.003
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    References listed on IDEAS

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    1. Jason Xu & Peter Guttorp & Midori Kato-Maeda & Vladimir N. Minin, 2015. "Likelihood-based inference for discretely observed birth–death-shift processes, with applications to evolution of mobile genetic elements," Biometrics, The International Biometric Society, vol. 71(4), pages 1009-1021, December.
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