Table of Contents 0. Studying Microbial Diversity 0. Getting started: the feature table 0. Terminology 0. Measuring alpha diversity 0. Observed species (or Observed OTUs) 0. A limitation of OTU counting 0. Phylogenetic Diversity (PD) 0. Even sampling 0. Measuring beta diversity 0. Distance metrics 0. Bray-Curtis 0. Unweighted UniFrac 0. Even sampling 0. Interpreting distance matrices 0. Distribution plots and comparisons 0. Hierarchical clustering 0. Ordination 0. Polar ordination 0. Determining the most important axes in polar ordination 0. Interpreting ordination plots 0. Tools for using ordination in practice: scikit-bio, pandas, and matplotlib 0. PCoA versus PCA: what's the difference? 0. Are two different analysis approaches giving me the same result? 0. Procrustes analysis 0. Where to go from here 0. Acknowledgements