Is there an easy/quick way to get the listing of species from a sharedotus file? I know the OTUs are all listed in cons.taxonomy - seems like there should be a way of going from sharedotu to a list of species…
Here’s a better way:
mothur > get.sharedseqs(shared=yourSharedFile, uniquegroups=yourGroups, label=yourLabel, output=accnos) - list OTU names in overlap in venn diagram. OTUs that contain the sequences from yourGroups.
mothur > get.otulabels(list=yourListFile, accnos=accnosFileFromGetSharedSeqs) - select those Otus from list file
mothur > get.otulabels(constaxonomy=yourConstaxonomyfile, accnos=accnosFileFromGetSharedSeqs) - select those Otus from constaxonomy file