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.

Getting started

Package details

AuthorSharon Bewick [aut, cre], Benjamin Camper [aut], National Science Foundation Division of Integrative Organismal Systems (award #2104605) [fnd]
Bioconductor views Software phyloseq
MaintainerSharon Bewick <sbewick@clemson.edu>
LicenseGPL-2
Version0.1.3
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("holobiont")

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holobiont documentation built on Aug. 8, 2025, 7:31 p.m.