indices_diversity

indices_diversity computes Chao, Simpson, and Shannon diversity indices from Sabund and Rabund formatted abundance tables to assess species richness and evenness in biological communities.

Key Features:

• Chao Index: Estimates total species richness from abundance data by accounting for rare species.
• Simpson Index: Quantifies the probability that two randomly selected individuals belong to the same species, reflecting dominance and diversity.
• Shannon Index: Measures the uncertainty in predicting the species identity of a randomly chosen individual, reflecting richness and evenness.
• Input formats: Accepts abundance tables in Sabund and Rabund formats.
• Next-generation DNA sequencing data: Supports analysis of large abundance datasets generated by next-generation DNA sequencing technologies.

Scientific Applications:

• Microbial community composition: Characterizes microbial community structure using diversity indices derived from sequencing abundance tables.
• Microbiome analysis: Enables diversity comparisons and summary statistics in microbiome studies based on sequencing data.
• Ecosystem health assessment: Quantifies species richness and evenness to inform assessments of ecosystem health.
• Biodiversity pattern analysis: Evaluates biodiversity patterns across environments or experimental conditions.
• Ecological genomics: Supports studies linking genetic or sequencing-derived data to ecological diversity metrics.

Methodology:

Computes Chao, Simpson, and Shannon indices directly from Sabund and Rabund abundance tables and integrates with the Galaxy project to record computational steps and provenance automatically.