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Amova (version 1.39.5.0)

phylip - Distance Matrix:

design - assign groups to new grouping:

design has 2 TAB-separated columns: group and grouping (Tool: Make_Design)

alpha - acceptable stopping precision:

default: 0.05

iters - Number of random configuration to try:

default: 1000

sets - Which of the sets in your design file you would like to analyze?:

separate sets by dashes or commas, e.g. set1,set2 or set1-set2-set3

Output logfile?:

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 amova command calculates the analysis of molecular variance from a phylip_distance_matrix, a nonparametric analog of traditional analysis of variance. This method is widely used in population genetics to test the hypothesis that genetic diversity within two populations is not significantly different from that which would result from pooling the two populations.

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.