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, which can be downloaded from the website
provided under Additional repositories.
