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Determine beta diversity

Beta diversity is a measure of diversity between samples. One of the most commonly used metrics is the Unifrac distance that compares samples using phylogenetic information. An all-by all or pairwise matrix of the beta diversity metrics between all the samples in the study is generated and can be visualized in different ways such as a tree, graph, network etc. Mothur and QIIME have several tools to generate distance metrics, phylogenetic trees and PCoA plots.

Software: UNIFRAC for distance metrics, mothur, QIIME