Morisitahorn
From mothur
The morisitahorn calculator returns the Morisita-Horn index describing the similarity between the structure of two communities. This calculator can be used in the summary.shared and collect.shared commands.
where,
SA,i = the number of individuals from community A in the ith OTU
SB,i = the number of individuals from community B in the ith OTU
n = the number of individuals in community A
m = the number of individuals in community B
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 | XY | X2 | Y2 |
|---|---|---|---|---|---|
| 1 | 1 | 0 | 0 | 1 | 0 |
| 2 | 1 | 0 | 0 | 1 | 0 |
| 3 | 1 | 0 | 0 | 1 | 0 |
| 4 | 1 | 1 | 1 | 1 | 1 |
| 5 | 1 | 0 | 0 | 1 | 0 |
| 6 | 1 | 0 | 0 | 1 | 0 |
| 7 | 3 | 1 | 3 | 9 | 1 |
| 8 | 3 | 0 | 0 | 9 | 0 |
| 9 | 2 | 0 | 0 | 4 | 0 |
| 10 | 2 | 5 | 10 | 4 | 25 |
| 11 | 1 | 0 | 0 | 1 | 0 |
| 12 | 1 | 0 | 0 | 1 | 0 |
| 13 | 3 | 0 | 0 | 9 | 0 |
| 14 | 2 | 0 | 0 | 4 | 0 |
| 15 | 1 | 0 | 0 | 1 | 0 |
| 16 | 1 | 3 | 3 | 1 | 9 |
| 17 | 1 | 0 | 0 | 1 | 0 |
| 18 | 1 | 0 | 0 | 1 | 0 |
| 19 | 2 | 0 | 0 | 4 | 0 |
| 20 | 1 | 3 | 3 | 1 | 9 |
| 21 | 1 | 0 | 0 | 1 | 0 |
| 22 | 2 | 0 | 0 | 4 | 0 |
| 23 | 5 | 2 | 10 | 25 | 4 |
| 24 | 1 | 1 | 1 | 1 | 1 |
| 25 | 1 | 0 | 0 | 1 | 0 |
| 26 | 1 | 1 | 1 | 1 | 1 |
| 27 | 1 | 0 | 0 | 1 | 0 |
| 28 | 2 | 0 | 0 | 4 | 0 |
| 29 | 1 | 0 | 0 | 1 | 0 |
| 30 | 1 | 0 | 0 | 1 | 0 |
| 31 | 1 | 0 | 0 | 1 | 0 |
| 32 | 1 | 0 | 0 | 1 | 0 |
| 33 | 1 | 1 | 1 | 1 | 1 |
| 34 | 0 | 2 | 0 | 0 | 4 |
| 35 | 0 | 1 | 0 | 0 | 1 |
| 36 | 0 | 1 | 0 | 0 | 1 |
| 37 | 0 | 1 | 0 | 0 | 1 |
| 38 | 0 | 1 | 0 | 0 | 1 |
| 39 | 0 | 1 | 0 | 0 | 1 |
| 40 | 0 | 7 | 0 | 0 | 49 |
| 41 | 0 | 1 | 0 | 0 | 1 |
| 42 | 0 | 1 | 0 | 0 | 1 |
| 43 | 0 | 2 | 0 | 0 | 4 |
| 44 | 0 | 1 | 0 | 0 | 1 |
| 45 | 0 | 1 | 0 | 0 | 1 |
| 46 | 0 | 1 | 0 | 0 | 1 |
| 47 | 0 | 1 | 0 | 0 | 1 |
| 48 | 0 | 1 | 0 | 0 | 1 |
| 49 | 0 | 1 | 0 | 0 | 1 |
| 50 | 0 | 1 | 0 | 0 | 1 |
| 51 | 0 | 1 | 0 | 0 | 1 |
| 52 | 0 | 1 | 0 | 0 | 1 |
| 53 | 0 | 2 | 0 | 0 | 4 |
| 54 | 0 | 1 | 0 | 0 | 1 |
| 55 | 0 | 1 | 0 | 0 | 1 |
| Total | 49 | 49 | 33 | 99 | 131 |
Using these sums to evaluate C we get:
Running...
mothur > summary.shared(calc=morisitahorn)
...and opening 98_lt_phylip_amazon.fn.shared.summary gives:
label comparison MorisitaHorn 0.10 forest pasture 0.286957
These are the same values that we found above for a cutoff of 0.10.
