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alpha_div command
Commands > OTU analysis, Diversity analysis

See also
alpha diversity metrics
  beta_div command

The alpha_div command calculates one or more alpha diversity metrics for each sample in an OTU table. The OTU table must be in QIIME classic format.

The -metrics option specifies one or more metric names separated by commas. Default is all metrics. See alpha diversity metrics for supported metrics.

Output is written to a table specified by the -output option. The file is in tabbed text format. Rows are samples, columns are metrics. This file can be loaded into spreadsheet software such as Excel for further analysis.

Example: calculate all metrics

usearch -alpha_div otutable.txt -output alpha.txt

Example: calculate Gini-Simpson index

usearch -alpha_div otutable.txt -output gini.txt -metrics gini_simpson

Example: calculate Chao1 and Berger-Parker indexes

usearch -alpha_div otutable.txt -output alpha.txt -metrics chao1,berger_parker