Remove bacterial sequences from Archeal dataset

Hi
I have 30-50% eubacterial rRNA gene sequences in my Archebacterial rRNA datasets. And I have several metagenic samples to deal with. Is there a way to remove these eubacterial sequences and clean up my data?
Thanks
srini

The following commands may help:

http://www.mothur.org/wiki/Get.lineage
http://www.mothur.org/wiki/Remove.lineage
http://www.mothur.org/wiki/Get.seqs
http://www.mothur.org/wiki/Remove.seqs
http://www.mothur.org/wiki/List.seqs

Hi Westcott
I could be able to separate Archebacterial sequences.
Thanks much for your suggestion.
Srini