<p>Note.— <i>p</i>: Number of parameters including 15 branch lengths in the tree (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003746#pone-0003746-g004" target="_blank">Figure 4</a>). Estimates of <i>κ</i> range from 3.4 to 3.6 among models. Sites potentially under positive selection are listed for different models, with the human sequence used as reference. The posterior probability <i>P</i> that a site is from the positive-selection class is calculated using BEB <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003746#pone.0003746-Yang4" target="_blank">[17]</a>.</p
<p>Note: ω = <i>d</i><sub>N</sub>/<i>d</i><sub>S</sub>; p and q: parameters of beta distribution;</...
Site-specific selection on NP inferred with the experimentally informed models. This figure is equiv...
<p>*<i>ω</i>0 is theratio of nonsynonymous-synonymous substitutions (<i>d</i><sub>N</sub>/<i>d</i><s...
<p>Likelihood ratio tests (−2Δ<i>l</i>) comparing a null and positive selection models (M1a vs M2a, ...
<p>lnL, the log-likelihood difference between the two models; 2Δl, twice the log-likelihood differen...
<p>Notes: positively selected sites with significance at the 99% level are bold, whereas the remaini...
<p>−2Δ<i>L</i>, likelihood ratio test to detect positive selection with 1 degree of freedom; Foregro...
<p>−2Δ<i>L</i>, likelihood ratio test to detect positive selection; p: proportion of sites under pos...
a<p>Twice the difference between the log likelihood of M0 (one ratio) and two ratio model.</p>b<p><i...
<p>Note: np number of parameters, ln<i>L</i> ln[likelihood] value, 2Δ(ln<i>L</i>) twice the differen...
<p><b>Note:</b><i>P</i> number of parameters in the <i>ω</i> distribution, <i>K</i> estimated transi...
<p>The branch lengths, in the expected number of nucleotide substitutions per codon, are estimated u...
<p>The likelihood values and the respective estimated parameters are shown for each model. The ω rat...
<p>−2Δ<i>L</i>, likelihood ratio test to detect positive selection; Foreground: <i>H. sapiens</i>, <...
a<p>Number of parameters.</p>b<p>Only positively selected sites with a posterior probability equal o...
<p>Note: ω = <i>d</i><sub>N</sub>/<i>d</i><sub>S</sub>; p and q: parameters of beta distribution;</...
Site-specific selection on NP inferred with the experimentally informed models. This figure is equiv...
<p>*<i>ω</i>0 is theratio of nonsynonymous-synonymous substitutions (<i>d</i><sub>N</sub>/<i>d</i><s...
<p>Likelihood ratio tests (−2Δ<i>l</i>) comparing a null and positive selection models (M1a vs M2a, ...
<p>lnL, the log-likelihood difference between the two models; 2Δl, twice the log-likelihood differen...
<p>Notes: positively selected sites with significance at the 99% level are bold, whereas the remaini...
<p>−2Δ<i>L</i>, likelihood ratio test to detect positive selection with 1 degree of freedom; Foregro...
<p>−2Δ<i>L</i>, likelihood ratio test to detect positive selection; p: proportion of sites under pos...
a<p>Twice the difference between the log likelihood of M0 (one ratio) and two ratio model.</p>b<p><i...
<p>Note: np number of parameters, ln<i>L</i> ln[likelihood] value, 2Δ(ln<i>L</i>) twice the differen...
<p><b>Note:</b><i>P</i> number of parameters in the <i>ω</i> distribution, <i>K</i> estimated transi...
<p>The branch lengths, in the expected number of nucleotide substitutions per codon, are estimated u...
<p>The likelihood values and the respective estimated parameters are shown for each model. The ω rat...
<p>−2Δ<i>L</i>, likelihood ratio test to detect positive selection; Foreground: <i>H. sapiens</i>, <...
a<p>Number of parameters.</p>b<p>Only positively selected sites with a posterior probability equal o...
<p>Note: ω = <i>d</i><sub>N</sub>/<i>d</i><sub>S</sub>; p and q: parameters of beta distribution;</...
Site-specific selection on NP inferred with the experimentally informed models. This figure is equiv...
<p>*<i>ω</i>0 is theratio of nonsynonymous-synonymous substitutions (<i>d</i><sub>N</sub>/<i>d</i><s...