LEfSe on familiy level?


is it possible to use the lefse implementation of mothur on family level instead of OTU level? Or is there an alternative to compare if famalies in two grpups have changed?


Sure - you would use the phylotype command and then generate a shared file. You could use that shared file as input to lefse. This is kind of outlined towards the end of the MiSeq SOP page.


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