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In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing

In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA. In each step of the search, we use parametric bootstraps and the Mahalanobis distance to estimate how well a proposed set of parameters fits input data. Using simulations, we demonstrate that our methodology can accurately infer the indel parameters for a large variety of plausible settings.

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    Date Created
    • 2015-11-03
    Resource Type
  • Text
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    Identifier
    • Digital object identifier: 10.1093/gbe/evv212
    • Identifier Type
      International standard serial number
      Identifier Value
      1759-6653
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    Karin, E. L., Rabin, A., Ashkenazy, H., Shkedy, D., Avram, O., Cartwright, R. A., & Pupko, T. (2015). Inferring Indel Parameters using a Simulation-based Approach. Genome Biology and Evolution, 7(12), 3226-3238. doi:10.1093/gbe/evv212

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