Background: Sequence-based phylogenetic trees are a well-established tool for characterizing diversity of both macroorganisms and microorganisms. Phylogenetic methods have recently been applied to shotgun metagenomic data from microbial communities, partic

Background: Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from t