I’m missing something with the Indicator command. For OTUs that are significant indicators, how is one to know for which group they are indicative?

This will be part of version 1.29.0

I have a query regarding Indicator command in mothur.
In the parameter option its mentioned that one can provide shared file and design file OR shared file and tre file.
why both combination gives different kind of output.
And other thing is when i ran the command with design file and shared file i got some indicators OTU’s which had mere one size.
Can anyone explains me why it consider OTU’s with significant p-value when the size of OTU is just one.

Thanks in advance

Mothur allows you to run the indicator command 2 ways. When you run it with a shared and design file, mothur uses the design file to determine the groupings and runs the algorithm for each OTU. When you run it with a tree and shared file the structure of the tree is used to determine the groupings. The algorithm is run at each node for each OTU. Running indicator(citation) will give you the papers referenced when coding the algorithm.

Thanks you!! It worked.
One more thing I would like to know is which statistical method has been used to find the indicator species.

Thanks in advance


mothur > indicator(citation)

Dufrene M, Legendre P (1997). Species assemblages and indicator species: The need for a flexible asymmetrical approach. Ecol Monogr 67: 345-66.
McCune B, Grace JB, Urban DL (2002). Analysis of ecological communities. MjM Software Design: Gleneden Beach, OR.
Legendre P, Legendre L (1998). Numerical Ecology. Elsevier: New York.