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Updated: Apr 25, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
treestructure: an R package to detect population structure in phylogenetic trees
Fabrícia F Nascimento1, Vinicius B Franceschi1, Erik M Volz1
1MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, W12 0BZ, United Kingdom.
Motivation:
How population structure can shape genetic diversity is a longstanding problem in population genetics. While the use of geographic locations, when available, can help answer some of these questions, it is still difficult to determine population structure when such metadata are not available or when the potential population structure is not easily observed. Here, we present an updated version of treestructure, an R package that implements a statistical test based on coalescent theory to detect unobserved population structure in a time-scaled phylogenetic tree.
Availability:
treestructure is available at CRAN at https://cloud.r-project.org/web/packages/treestructure/ and at https://emvolz-phylodynamics.github.io/treestructure/.
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