Hello
I am using mothur for my 16S rRNA data. I have several groups I want to compare statistically, however, the “mouse.time.design” in MiSeq SOP only compare two groups (Early vs. Late). I have tried to add more groups, but it does not work. It must be possible to add more than 2 groups in the design.file? It would be very helpful to see an example of a design.file in which several groups are included.
Thank you very much!
You would change the “Early” and “Late” to the names of the groups you are interested in. Can you post your design file and the error you are getting?
Pat
Great, thank you! It works fine when the groups are the same in both of these files “design.file” and “stability.an.thetayc.0.03.lt.ave.tre”. However, if I only want to include a subset of the groups from the file “stability.an.thtay…”, should I choose another size here: mothur > sub.sample(shared=stability.an.shared, size=2241), or should I make another “stability.file” and run all the steps from the beginning?
It is perhaps a way of specifying the groups to be used from the file “stability.an…” when I use this command:
parsimony(tree=stability.an.thetayc.0.03.lt.ave.tre, group=mouse.time.design, groups=all)? I tried to specify the groups in groups=cDNA10-cDNA11-cDNA12-cDNA13, but this does not work.
my design file is shown here:
group sample_type
cDNA10 mucosa_active_bacteria
cDNA11 mucosa_active_bacteria
cDNA12 mucosa_active_bacteria
cDNA13 mucosa_active_bacteria
cDNA14 mucosa_active_bacteria
cDNA15 mucosa_active_bacteria
cDNA16 mucosa_active_bacteria
cDNA17 mucosa_active_bacteria
cDNA18 mucosa_active_bacteria
cDNA19 mucosa_active_bacteria
cDNA1 mucosa_active_bacteria
cDNA20 mucosa_active_bacteria
cDNA21 mucosa_active_bacteria
cDNA22 mucosa_active_bacteria
cDNA23 mucosa_active_bacteria
cDNA24 mucosa_active_bacteria
cDNA25 mucosa_active_bacteria
cDNA27 mucosa_active_bacteria
cDNA2 mucosa_active_bacteria
cDNA42 mucosa_active_bacteria
cDNA5 mucosa_active_bacteria
cDNA6 mucosa_active_bacteria
cDNA7 mucosa_active_bacteria
cDNA8 mucosa_active_bacteria
fDNA10 faeces
fDNA11 faeces
fDNA12 faeces
fDNA13 faeces
fDNA14 faeces
fDNA15 faeces
fDNA16 faeces
fDNA17 faeces
fDNA18 faeces
fDNA19 faeces
fDNA1 faeces
fDNA20 faeces
fDNA21 faeces
fDNA22 faeces
fDNA23 faeces
fDNA24 faeces
fDNA25 faeces
fDNA26 faeces
fDNA27 faeces
fDNA28 faeces
fDNA29 faeces
fDNA2 faeces
fDNA30 faeces
fDNA31 faeces
fDNA3 faeces
fDNA4 faeces
fDNA5 faeces
fDNA6 faeces
fDNA7 faeces
fDNA8 faeces
fDNA9 faeces
mDNA10 mucosa
mDNA11 mucosa
mDNA12 mucosa
mDNA13 mucosa
mDNA14 mucosa
mDNA15 mucosa
mDNA16 mucosa
mDNA17 mucosa
mDNA18 mucosa
mDNA19 mucosa
mDNA1 mucosa
mDNA20 mucosa
mDNA21 mucosa
mDNA22 mucosa
mDNA23 mucosa
mDNA24 mucosa
mDNA25 mucosa
mDNA27 mucosa
mDNA2 mucosa
mDNA42 mucosa
mDNA5 mucosa
mDNA6 mucosa
mDNA7 mucosa
mDNA8 mucosa
Thank you 
The groups parameter in the parsimony command is used to select items from the second column of the group or design file. If you would like to select of remove groups from your files you can uses the get.groups and remove.groups commands. http://www.mothur.org/wiki/Get.groups http://www.mothur.org/wiki/Remove.groups
Great, that was very helpful, thank you very much