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Mantel

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The mantel command calculates the Mantel correlation coefficient between two matrices. Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman. To run the tutorial below please download the files and follow along...


Default Settings

The mantel command requires two phylip formatted distance matrices.

mothur > mantel(phylip1=veg.dist, phylip2=env.dist)

opening veg.mantel you would see:

Mantel	pValue
0.304745	0.001000

Options

method

The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.

mothur > mantel(phylip1=veg.dist, phylip2=env.dist, method=spearman)

opening veg.mantel you would see:

Mantel	pValue
0.283791	0.001000


mothur > mantel(phylip1=veg.dist, phylip2=env.dist, method=kendall)

opening veg.mantel you would see:

Mantel	pValue
0.189196	0.002000

iters

The default is 1000.