For hypothesis testing of site models with CCR3 gene sequences, the comparison of M1a (neutral) vs. M2a (selection) site models led to rejection of the null, neutral hypothesis in favor of selection with a likelihood test ratio statistic of 19.84, significant at p = 0.001, with a proportion of sites (0.01346 1%), and ω = 5.44115, indicating positive selection for those codon sites (Table 1).
†The posterior probability and P value in LRT with null hypothesis of the site are shown in parenthesis for the BEB and FEL analyses, respectively.
Hence, these similarities in terms of binding sites would strengthen the hypothesis of a site-direct antagonism between quercetin and crotoxin at nerve terminals.
More recently, Yuan and coworkers combined their ODE model with massive experimental data of metabolomics to investigate the hypothesis of active-site competition on GOGAT [17].
If the latter, these examples may more appropriately relate to the hypothesis of species-site mismatch (see above), but in the context of well-suited genotypes rather than species.
This is a very useful feature to quickly visualize multiple reconstruction-hypotheses of a site.
It was shown that of the three hypotheses of the site of insulin sensitivity change in the basal state, the hypothesis that the effect was mainly hepatic was the most robust.
This simulates the null hypothesis of neutrality: the site was not subject to selection.
To assess whether it is consistent or against the hypothesis of proto-spliced sites, we calculate the position distribution of four possible proto-splice sites (tested in [ 23, 24]) within human coding sequences, and the results are shown in Additional file 1: Figure S3.
Significance of the PHI statistic for the presence of recombination is assessed with the normal approximation of a permutation test where, under the null hypothesis of no recombination, sites along the alignment are randomly permuted to obtain the null distribution of PHI: p<0.05 indicate significant presence of recombination [69].
