Design files for AMOVA/HOMOVA

Hi- So I’m trying to run the AMOVA/HOMVA commands using a few different design files. I have 2 files that work that separate my samples by treatment or by time. (I have 6 replicate samples, with 4 different treatments at 4 different sampling time points, for a total of 96 samples). I want to be able to look at differences between treatments from each individual sampling time, and not across all sampling times. I made at design file to include those samples from just the desired sampling times, but I get an error saying “[ERROR]: 9NNT6 is not in your design file, please correct.” This error is shown for each sample that is not part of my desired set of sampling times. Any suggestions of how to get around this? I’m still pretty new to mothur so need the ‘idiot’s version’ of how to correct this!



Mothur is expecting all the samples in the distance file to be present in the design file. I assume you created the phylip file using dist.shared command. If that is the case, you can select the samples you would like to include in the distance file using the groups parameter of the dist.shared command.

dist.shared(shared=yourSharedFile, groups=samplesFromTheDesiredSamplingTime)

I hope this helps,

Thanks Sarah… I figured it out… I think… At least the results I got look good!