mantel

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.