get.oturep for a specific .group.rabund

Commands in mothur
1

Hi,

I am not able to put this together.
I have two groups of seqs. I got a rank abund for each group using the read.otu of .list from read.dist.
I also have the .shared file.

I got the rep fasta seqs belonging to each label by-
“#read.dist(phylip=J07site19CloneLib.phylip.dist);get.oturep(list=J07site19CloneLib.phylip.fn.list,fasta=J07site19CloneLib.fasta,group=J07site19CloneLib.groups,label=0.03-0.04-0.05);”
How do I get a rep fasta sequence belonging to each rank in a particular group. Or should I just run the analysis as single sample?

I feel like I have the info, but I am not able to put it together. Thanks for helping.

Priya

2

What you really want is a command to parse your list file, which is on the list for the next release. In the meantime here is a work around. If you create a file with the names of the sequences from the group you want, you can use the get.seqs command to create a list file with only those names in it. http://www.mothur.org/wiki/Get.seqs