Estimation of Alpha and Beta diversity

Two levels of diversity are typically considered in microbial ecology: alpha- and beta-diversity. Alpha-diversity estimates describe the number of species (or similar metrics) in a single sample, whereas beta-diversity compares the number of species (or similar metrics) across samples [Whittaker, 1972].

Some measures of estimate alpha and beta diversity require a phylogenetic tree of all OTUs. The phylogenetic tree is reconstructed based on a multiple sequence alignment (MSA) of the OTU sequences. Therefore, as a pre-requisite, a MSA needs to be created and a phylogeny reconstructed.


Subsections