Align OTUs with MUSCLE

To estimate Alpha and Beta diversity, OTUs must initially be aligned with the MUSCLE tool of the CLC Microbial Genomics Module:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Amplicon-Based Analysis (Image otutools_open_16_n_p) | Align OTUs using MUSCLE (Image alignment)

Choose an OTU abundance table as input. The next wizard window allows you to set up the alignment parameters with MUSCLE (figure 5.11).

Image muscleparameters
Figure 5.11: Set up parameters for aligning sequences with MUSCLE.

Note that by default only the top 100 most abundant OTUs are aligned using MUSCLE and used to reconstruct the phylogeny tree in the next step. This phylogenetic tree is used for calculating the phylogenetic diversity and the UniFrac distances, so these measures disregard the low abundance OTUs by default. If more OTUs are to be included, the default settings for the MUSCLE alignment need to be changed accordingly.

For further analysis with the Alpha and Beta diversity tools, save the alignment and construct a phylogenetic tree using the Maximum Likelihood Phylogeny tool (use the Launch button to find it in the Toolbox). For more information, see