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Homova (version
design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)

Mothur Overview

Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki.

Command Documentation

The homova command calculates the homogeneity of molecular variance (HOMOVA) from a phylip_distance_matrix, 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.

A design file partitions a list of names into groups. It is a tab-delimited file with 2 columns: name and group, e.g. :
duck bird
cow mammal
pig mammal
goose bird
cobra reptile

The Make_Design tool can construct a design file from a Mothur dataset that contains group names.

v.1.20.0: Updated to Mothur 1.33, added sets parameter