Microbiome & multi-omics / Alpha diversity
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Alpha diversity describes richness and evenness within each sample. Observed richness, Chao1 and ACE measure richness (Chao1 and ACE use taxa seen once or twice to estimate unseen taxa); Shannon, Simpson and inverse Simpson combine richness and evenness; Pielou measures evenness only.
Richness depends strongly on sequencing depth: when read totals differ a lot, tick “Rarefy to an even depth first”, or check the rarefaction curves. Rarefaction is random; a fixed seed makes it reproducible.
With a sample sheet, each index is tested with the Kruskal–Wallis test and pairwise comparisons (Dunn’s test or Wilcoxon rank-sum, adjusted for multiple testing); the plot marks only pairs with adjusted P < 0.05 (* < 0.05, ** < 0.01, *** < 0.001, **** < 0.0001).
Good’s coverage = 1 − singletons / total reads; values close to 1 mean most taxa have been sampled.
Index definitions follow scikit-bio diversity.alpha: Shannon (1948), Simpson (1949), Pielou (1966), bias-corrected Chao1 (Chao 1984), ACE (Chao & Lee 1992), Good (1953). Kruskal–Wallis matches scipy.stats.kruskal; Dunn’s test matches scikit-posthocs posthoc_dunn.
Up to 50,000 taxa.
Send us your data and research question and you will receive a written plan within 1 working day: analysis steps, parameter rationale, deliverables and timeline. Quoted per project.