I suppose this is a feature request if there is no other way of doing this.
Is there a way to get otu.hierarchy for individual groups within a groups file ?
I can run <get.groups> of the .list file, which will give me a list file for a specific group. I can then run otu.hierarchy on each list file and get the hierarchy. Problem is that the OTUs across groups are not synchronous - in other words the OTUs are based on the total in a given sample, not the whole dataset.
Hope this makes sense.
We have plans to add OTULabels to the list file to help with issues like this. Currently, mothur only labels the OTUs in a shared file. When you select groups, OTUs where no groups are present are eliminated. There is not a great way around this currently, but if you ran:
You would see the labels for the OTUs in each group in the new shared file, so you could correlate back to the original list file. The OTUs in the list file are in the same order as the shared file, so OTU001 relates to the first OTU in the list file. I hope this helps.