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The get.otus command selects otus containing sequences from a specific group or set of groups.
The group, list, label and either groups or accnos are required. The command will generate a *.pick.* file.
mothur > get.otus(groups=B-C, group=esophagus.groups, list=esophagus.fn.list, label=0.03)
or you may wish to list your groups in a file instead of manually typing them. This can be done by using an accnos file.
mothur > get.otus(accnos=esophagus.groups.accnos, group=esophagus.groups, list=esophagus.fn.list, label=0.03)
Both commands will output a new esophagus.fn.pick.0.03.list containing the 66 otus with sequences in groups B or C, and well as esophagus.pick.0.03.groups.