Alpha diversity measures
The available diversity measures are:
- Number of OTUs: The number of OTUs observed in the sample.
- Chao 1 bias-corrected:
.
- Chao 1:
.
- Simpson's index:
.
- Shannon entropy:
.
where
is the number of OTUs;
is the number of distinct OTUs observed in the sample;
is the number of OTUs for which only one read has been found in the sample;
is the number of OTUs for which two reads have been found in the sample; and
is the fraction of reads that belong to OTU
.
The following distances are also available:
- Phylogenetic diversity:
where
is the number of branches in the phylogenetic tree,
is the length of branch
;
is the proportion of taxa descending from branch
; and the indicator function
and
assumes the value of
if any taxa descending from branch
is present in the sample or
0 otherwise.