I have made trees by two methods. In one method, I did the subsampling and then made the tree as below:
dist.shared(shared=final.an.unique_list.0.03.pick.0.03.pick.shared, calc=thetayc-jclass, subsample=1617)
While in other method I did not do subsampling of data set and jumped to the tree.shared command.
Now I have two trees, one with subsampled data (i.e. normalized) and one without subsampling. I want to see if both trees are same or different using some stats, is it possible to do this in mothur and get a statistical significance of similarities or differences.
The reason I want to do this exercise is that I have some samples which have less than 1617 reads and if I do subsampling, i need to throw them off.
thanks in advance