Hope we have all enjoyed a wonderful Thanksgiving holiday.
Here I have a question about the parsimony and unifrac.unweighted/unifrac.weighted commands. In the Mothur SOP, the results of the commands of parsimony, unifrac.unweighted,
and unifrac.weighted are the same: There was clearly a significant difference between the clustering of the early and late time points.
However, when I ran my own data, I found that:
–The parsimony results indicate that there is no significant difference.
–The unifrac.unweighted/unifrac.weighted results indicate that: The difference is significant.
I understand that the parsimony ignores the branch length and unifrac.unweighted/unifrac.weighted command does. However, I am still not sure how to appropriately interpret the results.