Exercises 1. Modify positions.bf so that the transition/transversion ratio is different from lineage to lineage, but equal among codon positions (ie, all branches leading to species A have the same ts/tv ratio, regardless of the codon position, but that ratio can differ from the ratio for branches leading to species B). 2. Modify positions.bf so that (i) all four species in demo.seq are analyzed, and (ii) first and second codon positions are combined into a single partition.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002