See also
alpha diversity
metrics
beta_div command
The alpha_div command calculates one or more alpha
diversity metrics from 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