In addition to inferences about putative agents of selection along environmental gradients, these measurements allow hypotheses about variation in the strength of divergent selection among natural populations - where estimating the strength of divergent selection is otherwise difficult [e.g., [ 29]].
Therefore, in addition to Bayesian inference for combinatorial regulation, we also consider here a naive approximation that estimates the probability of combinatorial regulation by the product of individual TF binding probabilities. Figure 10 shows ROC results and the corresponding histograms for the two different methods.
All trees that were chosen to be depicted, have been subjected in addition to Bayesian inference with MrBayes 3.1.2 [ 84].
In addition to phylogenetic inference, a number of researchers have recently developed Bayesian MCMC software for coalescent-based estimation of demographic parameters from genetic data [ 2- 7].
In addition to provide inference for a couple of scenarios where Koyama and Chen's method breaks down, the resulting estimate appears to have certain advantage in terms of bias magnitude and confidence interval width in many cases.
The determined mean substitution rates were in good concordance with earlier studies on non-bat CoV that used maximum likelihood-based methods inon-bat CoVthatayesian inference (25, 26, 38, 40 ).
In addition to providing inference for a couple of scenarios where Koyama and Chen's method can be difficult to apply, the resulting estimate based on our method appears to have certain advantage in terms of inference properties in many numerical simulations.
7 In addition to the inference of cytochrome P450 (CYP) activity by reverse-transcription polymerase chain reaction, immunoblotting of microsomes, or in vitro metabolism of substrates, 12– 15 genome-wide transcript 16 and proteome data 17 are available on human fetal hepatocytes.
In addition to facilitating inferences about A. lyrata population history, our extensive data provide an excellent opportunity to compare levels and patterns of diversity between A. lyrata and its close congener A. thaliana.
In addition to providing the inference procedure of C3NET [ 33], the c3net package allows also a visualization of the inferred network by utilizing the igraph package [ 40].
