tree.shared

Commands in mothur
1

I’ve worked my data set to the point where I am ready to build a tree and I’m having problems with a few things here.

Here’s the steps I am using.
1.) dist.seqs(fasta=dusel.filter.unique.fasta, output=lt) — this generates my phylip distance matrix with no problems and generates a .dist file.

2.)read.dist(phylip=dusel.filter.unique.phylip.dist) — this command also appears to work with out issue.

3.)cluster(method=nearest) — as far as I know, I am getting this command to work properly. MOTHUR generates a .list, .sabund, and.rabun as expected.

4.)read.otu(dusel.filter.unique.phylip.nn.list, group=dusel.filter.names) — this is where funny things start to happen.

First in the mother window, it gives an error for every sequence in my data set. Then it will generate a .rabund file for every sequence in my dataset. I’m thinking it may have something to do with the group file, but I haven’t seen any .group files generated so I just used the .names file from the unique.seqs command.

5.) after this, I do enter tree.shared() and it generates a bunch of .TRE files.

I must be doing something wrong here. Any suggestions from anyone would be a lot of help!

Thanks folks
Jason Koch
SDSMT

2

4.)read.otu(dusel.filter.unique.phylip.nn.list, group=dusel.filter.names)

I think you mean:

read.otu(list=dusel.filter.unique.phylip.nn.list, group=dusel.groups)

[note the list= and dusel.groups] To make a group file you need to either use the trim.seqs or make.group commands or do it yourself (e.g. http://www.mothur.org/wiki/Sogin_data_analysis#Data_availability).

Hope this helps…

3

Thanks Dr. Schloss, I think this will help!

Jason