Shared OTUs Between Samples

OK, so I’m sure this question like this has been asked a million times, but let’s make it 1,000,001.

I have microbiome abundance data from 10 female birds and 10 male birds. Female bird 1 is in a monogamous relationship with male bird 1, but not 2 through 10 (these birds mate for life). I want to see which OTUs are shared between female bird 1 and male bird 1, female bird 1 and male bird 2, female bird 1 and male bird 3, etc. What is the best way to pull this off in mothur? There are so many commands that look like they might be the one (or ones) but I could use some guidance.


I think you may find these two commands helpful.

With the get.sharedseqs command, you will want to pay special attention to the uniquegroups and sharedgroups options.

Thanks a lot for your response. I will work with those two commands and hopefully get the answer I’m looking for.