• Benchmarking multi-rate codon models 

      Delport, Wayne; Scheffler, Konrad; Gravenor, Mike B.; Muse, Spencer V.; Pond, Sergei Kosakovsky (Public Library of Science, 2010-07-21)
      The single rate codon model of non-synonymous substitution is ubiquitous in phylogenetic modeling. Indeed, the use of a non-synonymous to synonymous substitution rate ratio parameter has facilitated the interpretation of ...
    • Codon test : modeling amino acid substitution preferences in coding sequences 

      Delport, Wayne; Scheffler, Konrad; Botha, Gordon; Gravenor, Mike B.; Muse, Spencer V.; Pond, Sergei L. Kosakovsky (PLOS Computational Biology, 2010-08)
      Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids ...
    • Correcting the bias of empirical frequency parameter estimators in codon models 

      Kosakovsky Pond, Sergei; Delport, Wayne; Muse, Spencer V.; Scheffler, Konrad (Public Library of Science -- PLOS, 2010-07)
      Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution. The equilibrium character distributions of these ...
    • Frequent toggling between alternative amino acids Is driven by selection in HIV-1 

      Delport, Wayne; Scheffler, Konrad; Seoighe, Cathal (Public Library of Science, 2008)
      Host immune responses against infectious pathogens exert strong selective pressures favouring the emergence of escape mutations that prevent immune recognition. Escape mutations within or flanking functionally conserved ...