holobiont - Microbiome Analysis Tools
We provide functions for identifying the core community
phylogeny in any microbiome, drawing phylogenetic Venn
diagrams, calculating the core Faith’s PD for a set of
communities, and calculating the core UniFrac distance between
two sets of communities. All functions rely on construction of
a core community phylogeny, which is a phylogeny where branches
are defined based on their presence in multiple samples from a
single type of habitat. Our package provides two options for
constructing the core community phylogeny, a tip-based
approach, where the core community phylogeny is identified
based on incidence of leaf nodes and a branch-based approach,
where the core community phylogeny is identified based on
incidence of individual branches. We suggest use of the
microViz package.
