Beta Diversity

Beta diversity examines the change in species diversity between ecosystems. The analysis is done in two steps. First, the tool estimates a distance between each pair of samples (see Beta diversity measures). Once the distance matrix is calculated, the beta diversity analysis tool performs Principal Coordinate Analysis (PCoA) on the distance matrices. These can be visualized by selecting the PCoA icon (Image 3d_pcoa_16_n_p) in the bottom of the Beta Diversity results (Image pcoa_otu_16_n_p).

If you are working with an OTU table, you can specify an appropriate phylogenetic tree for computing phylogenetic diversity. In that case, you must have aligned the OTUs and constructed a phylogeny before running the Beta Diversity tool.

To run the tool, open

        Metagenomics (Image wma_folder_open_flat_16_n_p) | Abundance Analysis (Image abundance_folder_closed_16_n_p) | Beta Diversity (Image beta_diversity_16_n_p)

Select an abundance table with more than one sample as input (i.e., an OTU table table, or a merged functional or profiling table) and set the parameters for the beta diversity analysis as shown in figure 9.4.

Image betadiversityparameters
Figure 9.4: Set up parameters for the Beta diversity tool.

The output of the tool is a 3D PCoA plot (figure 9.5) that can also be seen as a table.

Image betadiversitypcoa
Figure 9.5: Beta diversity results seen as a 3D PCoA.

Use the settings in the right hand side panel to explore the results and visualize them adequately.



Subsections