Homogeneity of molecular variance (HOMOVA) is a nonparametric analog of Bartlett’s test for homo- geneity of variance, which has been used in population genetics to test the hypothesis that the genetic diversity within two or more populations is homogeneous (Stewart and Excoffier, 1996); this test has not been used in the microbial ecology litera- ture. The HOMOVA statistic is calculated by

\[B=\frac{\left (N-P\right)\ln\left(\frac{SS_W}{N-P}\right)-\sum_{i=1}^P\left(N_i-1\right)\ln\left(\frac{SS_{Wi}}{N_i-1}\right)}{1+ \frac{1}{3\left(P-1\right)}\left(\sum_{i=1}^P\frac{1}{N_i-1}-\frac{1}{N-P}\right)}\]

where N is the total number of sequences in the study, P is the number of treatments, Ni is the number of sequences in treatment i, and SSWi is the amount of SSW contributed by treatment i. The P-value of the observed B is determined by measuring the fraction of 1000 randomizations of the rows and columns in the distance matrix, where the observed B is greater than or equal to the randomized B-values. Those P-values less than 0.05 were considered significant.

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 homova.

mothur > homova(phylip=amazon.dist, design=amazon.design)

opening the amazon.homova file you will see:

HOMOVA BValue  P-value SSwithin_values
A-B    0.000158784 0.979   2.36007 2.36871



The default for the alpha parameter is 0.05.


The default for iters is 1000.


The sets parameter allows you to specify which of the sets in your design file you would like to analyze. The set names are separated by dashes. The default is all sets in the design file.