Sobs
The sobs calculator returns the number of observed OTUs for an OTU definition. This calculator can be used in the summary.single, collect.single, and rarefaction.single commands. Open the file 98_lt_phylip_amazon.fn.sabund generated using the Amazonian dataset with the following commands:
mothur > cluster(phylip=98_lt_phylip_amazon.dist, cutoff=0.10)
The 98_lt_phylip_amazon.fn.sabund file is also outputted to the terminal window when the cluster() command is executed:
unique 2 94 2
0.00 2 92 3
0.01 2 88 5
0.02 4 84 2 2 1
0.03 4 75 6 1 2
0.04 4 69 9 1 2
0.05 4 55 13 3 2
0.06 4 48 14 2 4
0.07 4 44 16 2 4
0.08 7 35 17 3 2 1 0 1
0.09 7 35 14 3 3 0 0 2
0.10 7 34 13 3 2 0 0 3
The first column is the label for the OTU definition and the second column is an integer indicating the number of sequences in the dominant OTU. Sobs is then calculated by summing the remaining columns. For example, sobs for an OTU definition of 0.10 would be calculated as:
\[S_{obs} = 34 + 13+ 3 + 2 + 0 + 0 + 3 = 55\]Running...
mothur > summary.single(calc=sobs)
...and opening 98_lt_phylip_amazon.fn.summary gives:
label sobs
unique 96.000000
0.00 95.000000
0.01 93.000000
0.02 89.000000
0.03 84.000000
0.04 81.000000
0.05 73.000000
0.06 68.000000
0.07 66.000000
0.08 59.000000
0.09 57.000000
0.10 55.000000 <---
These are the same values that we found above for a cutoff of 0.03.