I think I’m stuck here. I received an alignment from someone in a .txt format. I was able to use Phylip to make my distance matrix and analyze in DOTUR but now I want to look at the shared sequences between clone libraries; I have 3 groups to look at. Since I already had the alignment and everything, I went into excel and made my groups file with the name and group letter, saved as tab delimited .txt, which I changed to a .groups. When I go in to Mothur to do anything related to groups, it doesn’t work. When I try just a simple
mothur > read.otu(list=week.fn.list, group=week.groups)
I get a shared file with nothing in it and only one rabund file. I think it’s a group file issue. Can anyone help me?
Mothur has the capability of reading in alignments (granted it has to be in the right format), building distance matrices, and clustering OTU’s. Why don’t you try using Mothur instead of trying to translate between multiple programs (and multiple generations of programs 
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I have used the same technique for generating group files, so that shouldn’t be the problem.
Try running: summary.seqs(fasta=youralignmentfile.txt)
If it correctly reports back the number of sequences and number of alignment spaces in your file you should be g2g.
-Ryan
Yeah, I agree with Ryan. There’s a lot that could be going on here. Some things to try…
- Are there any spaces in your sequence or group names? The only spaces you should have in the group file are the tabs separating the sequence name from the group name
- Are you using the most recent version of mothur? mothur will tell you which sequences aren’t found in the group or list file.
- Always feel free to email us a copy of your list and group file and we can take a look (mothur.bugs@gmail.com)
Thanks. I try those things and see what happens.
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