Sentence examples for using the beb procedure from inspiring English sources

The sites under selection in the foreground branches were obtained after calculating probabilities of site classes using the BEB procedure.

Next, we applied the branch-site model to estimate the fraction of codons that are likely to have evolved under positive selection specifically in the five avian branches using the BEB procedure implemented in PAML.

Posterior probabilities (Qks) were calculated using the BEB method [ 65].

M2a and M8 identified one and seven sites, respectively, with an ω > 1 using the BEB method (Table 1).

Using the beb method we were able to highlight 17 and 32 sites in branches D1a and D1b, respectively.

Up to seven amino acid sites were identified as sites of positive selection using the BEB analysis in MAT1-1-3 but oney one site had strong support with BEB posterior probability > 95% in model M8 (see Additional file 3).

Only sites that are found to have a posterior probability (PP) > = 0.90 using the BEB method are reported, therefore reducing the probability of false positives [ 48].

The posterior probabilities associated with specific codons falling into a site class affected by positive selection were calculated using the BEB method, described by Yang et al. [ 105].

Using the beb method, we were able to detect 6 and 40 sites under positive selection in D2a and D2b, respectively.

Using the beb (Bayes empirical Bayes) method we identified 26 and 22 sites in branches D1a and D1b respectively, with high posterior probability to have evolved under positive selection.

There were no individual sites using the BEB calculation that had a PP > 0.90 of being positively selected under the CladeC model, therefore we applied modelA to gain more site-specific information.