until the method inferred an error rate of <0.05% in the OG data set (at tensomes).
Our method infers a non-redundant set of processes and their perturbed links, which we call a Biological Process Network (BPN), from the interactions between the observed perturbed genes.
Their phylogenies reconstructed using neighbor joining and maximum likelihood methods inferred a sister group relationship between S. nodorum and Eurotiomycetes in line with our supertree inference.
In addition, all three ancestral state reconstruction methods inferred a fourth amino acid change on the anthropoid stem that was not identified by the branch site test: a methionine to isoleucine at residue 33.
This statistical method infers an average response over the population and takes into account the between-subjects effect to prevent overestimation of standard errors for the time-dependent predictors due to repeated measurements [ 30].
It is notable that our finding that the BEST method inferred similar major clades as the concatenated methods, but inferred a different branching order among these major clades, has also been observed in other studies [ 40].
In comparison, the Gaussian model eliminated all targets as non-significant, while the fold-change method inferred the same 10 targets as our method, but also inferred an additional 8 targets, none of which have evidence of binding SB-202190 (Figure 4a and Table S1).
The first method infers a history of coevolution from current character displacement by comparing traits in the species of interest when they do co-occur (sympatric populations) with areas where they do not co-occur (allopatric populations, e.g. Schluter and Grant 1982; Schluter and McPhail 1992).
Using this method, we inferred a total of 61 type-I interferon genes with intact ORFs from the whole-genome shotgun trace archives for two chiropteran species, Pteropus vampyrus and Myotis lucifugus.
Using these methods, we inferred a tentative identity for a total of 522 unidentified ESTs, which represented 17% of the 3039 unidentified ESTs.
