groups file problem


I am a first time Mothur user. I have 454 sequence libraries for 16s and several functional genes that I would like to analyze. I used the first part of the SOP to initially process my sequences. I was able to create a groups file with the shhh.flows command. I was able to go as far as the unique.seqs command and then I moved over the RDP to translate and then align my sequences. They have some great tools for functional genes. Then I made a distance matrix using the phylip protdist command. I next wanted to make an OTU table in mothur, which I have able to do with the cluster command. Next, I wanted to use the single.rarefaction command with the group option, however I get an error message since my group file does not reflect the current since redundant sequences were removed. Can you advice how I can update the group file? Also, how can I be sure to include all the redundant sequences when performing other phylogenetic analysis. I have looked through the protein coding analysis examples but they do not address how to update the group file. I also do not have access to ARB at the moment which many of those examples use. Any advice on how to go about this or perhaps there are other tutorials available for functional genes. Thanks for your help!


The redundant sequence names are maintained in the “names” files. Are you including this when you run cluster?