alpha_div command

See also
Alpha diversity
alpha diversity metrics
Recommended alpha and beta metrics
Comparing alpha diversity between groups
alpha_div_sig command
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 .

To calculate the statistical significance of a change in metric between groups, use the alpha_div_sig command .

The -metrics option specifies one or more metric names separated by commas. Default is a few popular metrics. Popular does not necessarily mean recommended. 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 default 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