A Review of Approaches for Optimizing Phylogenetic Likelihood Calculations

  title={A Review of Approaches for Optimizing Phylogenetic Likelihood Calculations},
  author={Alexandros Stamatakis},
  journal={Bioinformatics and Phylogenetics},
  • A. Stamatakis
  • Published 2019
  • Biology
  • Bioinformatics and Phylogenetics
The execution times of likelihood-based phylogenetic inference tools for Maximum Likelihood or Bayesian inference are dominated by the Phylogenetic Likelihood Function (PLF). The PLF is executed millions of times in such analyses and accounts for 85–95% of overall run time. In addition, storing the Conditional Likelihood Vectors (CLVs) required for computing the Phylogenetic Likelihood Function largely determines the associated memory consumption. Storing CLVs accounts for approximately 80% of… 

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