Related Experiment Video
Updated: Sep 20, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
phyloMDA: an R package for phylogeny-aware microbiome data analysis
Tiantian Liu1, Chao Zhou1, Huimin Wang2
1SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China.
Background:
Modern sequencing technologies have generated low-cost microbiome survey datasets, across sample sites, conditions, and treatments, on an unprecedented scale and throughput. These datasets often come with a phylogenetic tree that provides a unique opportunity to examine how shared evolutionary history affects the different patterns in host-associated microbial communities.
Results:
In this paper, we describe an R package, phyloMDA, for phylogeny-aware microbiome data analysis. It includes the Dirichlet-tree multinomial model for multivariate abundance data, tree-guided empirical Bayes estimation of microbial compositions, and tree-based multiscale regression methods with relative abundances as predictors.
Conclusion:
phyloMDA is a versatile and user-friendly tool to analyze microbiome data while incorporating the phylogenetic information and addressing some of the challenges posed by the data.
Related Concept Videos
Phylogeny
Applications of Molecular Taxonomy
Evolutionary Relationships through Genome Comparisons
Modern Molecular Taxonomy
Phylogenetic Trees
Microbial Classification System

