alpha diversity metrics
Recommended alpha and beta metrics
Comparing alpha diversity between groups
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