Putting It All Together: positions.bf As an example of the type of analysis Hy-Phy was designed to implement, we now describe the batchfile positions.bf. This file illustrates some of the features of the CreateFilter command by ignoring species C and by creating separate filters for each of the three codon positions. The HKY85 model is used as the basic substitution model. First, the entire data set is analyzed in the normal way, treating all sites in the same way. A second LikelihoodFunction is then created, which splits the data according to codon position. Each of the three partitions is allowed to evolve with a separate rate. However, the transition/transversion ratio is constrained to be the same for all three codon positions as well as for all lineages. The likelihood ratio test statistic comparing these two models is computed, and the statistical significance of the test is reported using both the chi-squared approximation and nonparametric bootstrapping. The file positions.bf is rather complicated, so we will focus only on some of its key features. Using ``combs'' when filtering data. Define a substitution model for each position. Define two likelihood functions Estimate the P-value via parametric bootstrapping Exercises
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002