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Since the homogenous model (m0) is specified (model = 0 and nssites = 0), the same ω value (0.3357) is reported for each branch under the column dn/ds (see bold values above). We then describe how to use the codeml program of the paml package for phylogenetic analysis to calculate the dn / ds and how to perform some statistical tests for positive selection. In this exercise you will investigate the sensitivity of your estimate of ω to the other parameters in the model, in particular transition/transversion ratio (κ), and assumed model for codon frequencies (πi’s).

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Using the output of your best model m1a or m2a you can check how many sites belong significantly to the first class of sites (w<1), this may be a solution The model we use also estimates rate variation among codons, to account for selection at the dna level (davydov et al However if you want an answer for the full gene, you may do a branch test with

Wanted branched fixed (w=1) h1

For example, if nonsynonymous mutations are deleterious, purifying selection will reduce their fixation rate and dn/ds will be less than 1, whereas if nonsynonymous mutations are advantageous, they will be fixed at a higher rate than synonymous mutations, and dn/ds will be greater than 1. The second model is called m2a, and allows each position to chose between three possible values for omega, namely omega = 1 (neutral evolution), omega < 1 (purifying selection) and omega > 1 (positive selection), the two latter ones being estimated. Under purifying selection, natural selection prevents the replacement of amino acids, so the dn will be lower than the ds, and dn/ds < 1 And under positive selection, the replacement rate of amino acid is favoured by selection, and dn/ds > 1.

I am fitting the mg94 model with a global value for dn/ds using the fitmg94.bf One thing i was hoping to do was to get a global estimate of dn and ds separately, equivalent to the tree length for ds and tree length for dn values returned by the equivalent analysis in paml/codeml. The parameter of interest to us is ω = dn/ds, which indicates selective pressure