Define a substitution model for each position. The next portion of positions.bf creates a vector of observed frequencies for each of the filters using standard syntax. Next, the basic substitution model is defined. We use the HKY85 model, with trnasversion parameter b and global transition/transversion ratio R. A separate Model is created for each partition, since they each use different frequencies: global R; HKY85RateMatrix = {{*,b,R*b,b}{b,*,b,R*b}{R*b,b,*,b}{b,R*b,b,*}}; Model HKY85 = (HKY85RateMatrix, obsFreqs); Tree myTree = (a,b,og); Model HKY851 = (HKY85RateMatrix, obsFreqs1); Tree myTree1 = (a,b,og); Model HKY852 = (HKY85RateMatrix, obsFreqs2); Tree myTree2 = (a,b,og); Model HKY853 = (HKY85RateMatrix, obsFreqs3); Tree myTree3 = (a,b,og);
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002