Site analysis. Selective pressures and Likelihood-ratio-tests in protamine 1 and protamine 2 sequences.

Parameter estimation and likelihood scores under models of variable ω ratios among sites for protamine 1, cleaved region of protamine 2 and the mature form of protamine 2. The data have N sequences, each of Lc codons after alignment gaps are removed. Differences between log-likelihood values of models with 99% statistical significance level for 2 d. f. are indicated in ** and with 95% of statistical significance in *. The proportion of sites under positive selection (p1), or under selective constraint (p0) and parameters p and q for the beta distribution are given. Positively selected sites (PSS) with a posterior probability >0.95 (*) and >0.99 (**) in a Bayes Empirical Bayes are indicated. Selectives pressures are shown as proportion of amino acid sites for different classes of selective regimes. Class 1: sites under purifying selection (0<ω<1); Class 2: sites neutrally evolving (ω = 1); Class 3: sites subject to positive selection or relaxation (ω>1). Proportions of sites in each selective class were also calculated for DNA-anchoring domains, phosphorylation motifs and cleaving sites.