Alpha diversity measures

The available diversity measures are:

where $ n$ is the number of OTUs; $ D$ is the number of distinct OTUs observed in the sample; $ f_1$ is the number of OTUs for which only one read has been found in the sample; $ f_2$ is the number of OTUs for which two reads have been found in the sample; and $ p_i$ is the fraction of reads that belong to OTU $ i$.

The following distances are also available:

where $ n$ is the number of branches in the phylogenetic tree, $ b_i$ is the length of branch $ i$; $ p_i$ is the proportion of taxa descending from branch $ i$; and the indicator function $ I(p_i>0)$ and $ I(p_i^B>0)$ assumes the value of $ 1$ if any taxa descending from branch $ i$ is present in the sample or 0 otherwise.