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Anosim

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Referenced: Clarke, K. R. (1993). Non-parametric multivariate analysis of changes in community structure. _Australian Journal of Ecology_ 18, 117-143.

To run the tutorial below please download the files and follow along...


Default Settings

The phylip and design parameter are required. The phylip option allow you to enter your phylip formatted distance matrix. The design parameter allows you to assign your samples to groups when you are running anosim.

mothur > anosim(phylip=dune.dist, design=dune.design)

opening the dune.anosim file you will see:

comparison	R-value	P-value
BF-HF-NM-SF	0.257871	0.007*
BF-HF	0.14359	0.247
BF-NM	0.228395	0.116
BF-SF	0.265432	0.127
HF-NM	0.334667	0.056
HF-SF	0.148	0.115
NM-SF	0.384259	0.009
 

Options

alpha

The default for the alpha parameter is 0.05.

iters

The default for iters is 1000.