get groups at unifrac

Commands in mothur
1

Dear all,

I am working with a huge amount of samples that were amplified using 454. I constructed a design file to analyze the significant different among the groups, but I would like to analyzed only some of the groups using the option groups=A-B-C. May anyone help me to do that?
One more thing, due to the high number of samples (>300) we are working with, we named them as sample1, sample2,but now it is been really difficult to identified them in the dendrograms, as we are comparing 5 different condition. Any suggestions??

Many thanks

2

I assume your tree looks something like: ((sample1:0.48538, sample2:0.48538):0.0120768,(((sample3:0.0561495, sample4:0.0561495)…

and your design file looks something like:

sample1 A
sample2 A
sample3 B
sample4 C
sample5 D
…

If you want mothur to only consider samples from the groups A, B and C, set groups=A-B-C.

mothur > unifrac.weighted(tree=yourTreeFile, group=yourDesignFile, groups=A-B-C)