Alpha diversity is used to measure the diversity within a sample or an ecosystem. The two most commonly used alpha-diversity measurements are Richness (count) and Evenness (distribution). MicrobiomeAnalyst provides many metrics to calculate diversity within samples. Most commonly used ones are listed below:

• Observed: It estimates the amount of unique OTUs found in each sample (richness).
• ACE and Chao1: They considers observed OTUs with account for unobserved species based on low-abundance OTUs (richness).
• Shannon, Simpson and Fisher: These metrics accounts for both richness and evenness.
• Faith's PD: Phylogenetic Diversity measures the total branch length spanning all taxa present in a sample. Requires a phylogenetic tree.