4 Preliminary OTU analysis using Mothur

The preliminary analysis (alpha_beta_diversity rule) is part of the bioinformatics analysis. It includes:

• Creating reads count for each group.
• Subsampling for downstream analysis.
• Rarefaction.
• Computing Alpha diversity metrics.
• Computing Beta diversity metrics.
• Getting sample distances.
• Constructing sample phylip tree.
• Generating ordination matrices including PCoA and NMDS.
• More as needed…