Sharednseqs

The sharednseqs calculator returns the number of individuals sampled from two communities. This calculator can be used in the summary.shared and collect.shared commands.

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()
mothur > read.otu(list=98_lt_phylip_amazon.fn.list, group=amazon.groups, label=0.10)

The 98_lt_phylip_amazon.fn.shared file will contain the following two lines:

0.10   forest  55  1   1   1   1   1   1   3   3   2   2   1   1   3   2   1   1   1   1   2   1   1   2   5   1   1   1   1   2   1   1   1   1   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   
0.10   pasture 55  0   0   0   1   1   0   1   0   0   5   0   0   0   0   0   2   0   0   0   3   0   0   2   1   0   1   0   0   0   0   0   0   1   2   1   1   1   1   1   7   1   1   2   1   1   1   1   1   1   1   1   1   2   1   1   

This indicates that the label for the OTU definition was 0.10. The first line is from the forest sample and the second is from the pasture sample. There are a total of 55 OTUs between the two communities. Writing the data in a more presentable manner we see:

index forest pasture ——- ——– ——— 1 1 0 2 1 0 3 1 0 4 1 1 5 1 0 6 1 0 7 3 1 8 3 0 9 2 0 10 2 5 11 1 0 12 1 0 13 3 0 14 2 0 15 1 0 16 1 3 17 1 0 18 1 0 19 2 0 20 1 3 21 1 0 22 2 0 23 5 2 24 1 1 25 1 0 26 1 1 27 1 0 28 2 0 29 1 0 30 1 0 31 1 0 32 1 0 33 1 1 34 0 2 35 0 1 36 0 1 37 0 1 38 0 1 39 0 1 40 0 7 41 0 1 42 0 1 43 0 2 44 0 1 45 0 1 46 0 1 47 0 1 48 0 1 49 0 1 50 0 1 51 0 1 52 0 1 53 0 2 54 0 1 55 0 1 Total 49 49

So it is obvious that the number of sequences sampled between the two communities at a 0.10 cutoff was 98.

Running...

mothur > summary.shared(calc=sharednseqs)

...and opening 98_lt_phylip_amazon.fn.shared.summary gives:

label  comparison      SharedNSeqs
0.10   forest  pasture     98.000000

These are the same values that we found above for a cutoff of 0.10.