For each gene, phylogenetic trees were inferred by using maximum-likelihood and Bayesian inference methods.
Phylogenetic trees were inferred by maximum likelihood (ML), Neighbour joining (NJ), and Bayesian inference (BI).
Interactions were inferred by means of mutual information calculations for a selected quantitative feature.
Functions for both positively and negatively selected sites were inferred by annotating these sites with experimentally verified amino acid sites.
The dependence of microbial activities on basic soil characteristics were inferred by separately designed general linear models.
Differentially expressed genes were inferred by univariate statistical analysis.
Specific amino acid changes along the internal branches of the tree were inferred by maximum likelihood.
Demographic histories were inferred by a pairwise mismatch distribution analysis [40] (Figure 3).
Phylogenetic trees were inferred by using maximum-likelihood (ML) and Bayesian methods.
Dispersal patterns were inferred by examining the geographical structuring of relatedness using spatial autocorrelation analysis.
All orthologous gene pairs between species were inferred by reciprocal best hit (e-value 10−3).
