Statistical analysis (amova, homova)

I’d like to make some statistical analysis from my data which consists in treatment/control in 3 different time point first/third/fifth day (like an repeated measure approach). However I’m not sure how create design.file to input on amova and homova command. Should I create a tab-format table with 3 columns: name of group, treatment/control and time?
Another point is regarding hypothesis application: so, amova and homova are applied with repeat measure data, aren’t they?

thanks a lot,

I wouldn’t attempt to do that kind of stats within mothur. Take you data into another program (like R) and use more flexible tools.

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mothur’s amova/homova are implemented for use with simple, single single classification, experimental designs. If you have nesting, multiple factors, covariates, repeated measures, etc. you’re best served by the adonis function within the vegan R package.