Nseqs
The nseqs calculator returns the number of sequences that were sampled for an OTU definition. This calculator can be used in the summary.single, collect.single, and rarefaction.single commands, but it probably only really makes sense for the summary.single command. Open the file 98_lt_phylip_amazon.fn.sabund generated using the Amazonian dataset with the following commands:
mothur > read.dist(phylip=98_lt_phylip_amazon.dist, cutoff=0.10)
mothur > cluster()
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. The third column indicates the number of OTUs with only one indivdiual, the fourth the number of OTUs with two individuals, etc. Nseqs is then calculated by summing the product of the column index and the value in the column. For example, Nseqs for an OTU definition of
0.10 would be calculated as:
\[N = 34\left(1\right) + 13 \left(2\right) + 3 \left(3\right) + 2 \left(4\right) + 0 \left(5\right) + 0 \left(6\right) + 3 \left(7\right) = 98\]Running...
mothur > summary.single(calc=nseqs)
...and opening 98_lt_phylip_amazon.fn.summary gives:
label NSeqs
unique 98.000000
0.00 98.000000
0.01 98.000000
0.02 98.000000
0.03 98.000000
0.04 98.000000
0.05 98.000000
0.06 98.000000
0.07 98.000000
0.08 98.000000
0.09 98.000000
0.10 98.000000 <---
These are the same values that we found above for a cutoff of 0.03.