Related Experiment Video
Updated: Apr 14, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
phylogeo: an R package for geographic analysis and visualization of microbiome data
Zachary Charlop-Powers1, Sean F Brady1
1Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA.
Motivation:
We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language.
Availability And Implementation:
phylogeo is documented and freely available http://zachcp.github.io/phylogeo
Contact:
: zcharlop@rockefeller.edu.
Related Concept Videos
Microbial Phylogeny
Selected Data About Geographic Locations
Evolutionary Relationships through Genome Comparisons
Phylogenetic Species Concept in Microbiology
Phylogeny
Methods to Assess Microbial Communities

