• Detecting individual sites subject to episodic diversifying selection 

      Murrell, Ben; Wertheim, Joel O.; Moola, Sasha; Weighill, Thomas; Scheffler, Konrad; Pond, Sergei L. Kosakovsky (Public Library of Science, 2012-07-02)
      The imprint of natural selection on protein coding genes is often difficult to identify because selection is frequently transient or episodic, i.e. it affects only a subset of lineages. Existing computational techniques, ...
    • Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution 

      Murrell, Ben; Weighill, Thomas; Buys, Jan; Ketteringham, Robert; Moola, Sasha; Benade, Gerdus; du Buisson, Lise; Kaliski, Daniel; Hands, Tristan; Scheffler, Konrad (PLOS, 2011-12-22)
      Models of protein evolution currently come in two flavors: generalist and specialist. Generalist models (e.g. PAM, JTT, WAG) adopt a one-size-fits-all approach, where a single model is estimated from a number of different ...