Incorporating phylogenetic

Phylogenetically informed distances are commonly used in the analysis of microbiome data, and analysts have many options to choose from. Although all phylogenetic distances share the goal of incorporating the phylogenetic relationships among the bacteria, they do so in different ways and give different pictures of the relationships between the bacterial communities.

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RNAalifold, a popular computational method for RNA consensus structure prediction, incorporates covarying mutations into a thermodynamic model to fold the aligned RNA sequences. When quantifying covariance, it evaluates conserved signals of two aligned columns with base-pairing rules.

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Transcriptional gene regulation is a fundamental process in nature, and the experimental and computational investigation of DNA binding motifs and their binding sites is a prerequisite for elucidating this process.

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Evolutionary biology and ecology share the goals of describing variation in natural systems and discovering its functional basis. Within this common framework, evolutionary biologists emphasize historical and lineage-dependent processes and hence often incorporate phylogenetic reconstructions and genetic models in their analyses. Ecologists, while cognizant of historical processes, tend to explain variation in terms of the contemporary effects of biotic and abiotic environmental factors.

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