pulling out phylotype sequences

The classification of the OTU’s that were identified in my samples often only goes to the family level. I would like to get a representative sequence for these phylotypes and then blast them and analyze them further to attempt to increase the taxonomic level that they are classified at. I have tried to use the get.oturep command (egs. get.oturep(column=xyz.dist, name=xyz.names, list=xyz.an.list)) however the output from this command didn’t have any sequence data from what I could see. What I really want to do is get the representative sequences listed in the .tx.list file. Any help/guidance would be greatly appreciated

If you include your fasta file with the get.oturep command mothur will create a fasta file with the representative sequence for each otu. http://www.mothur.org/wiki/Get.oturep#fasta

Great! That worked for pulling out sequences using the xyz.an.list file. Is there a way to do the same thing to representative sequences after the OTUs have been classification into phylotypes? i.e. I would like to use the xyz.tx.list file. I hope that makes sense.
Thanks so much for your help I really appreciate it!

You can run get.oturep with the *.tx.list file for the list parameter.