These are the output files for the exercise using PAML to detect adaptive evolution.

mhc.out1278 is the site variation analyses with models 0, 1, 2, 7, 8.

mhc.outlineage is the lineage analyses with estimating dn/ds ratios for each lineage. Compare this to the model 0 from the file mhc.out1278.

mhc.pair is pairwise estimates of dn/ds.

mhc.pairw1 is the pairwise analysis with dn/ds = 1.