Hi Se Jin,
Yes, alpha_diversity.py worked with those files, too. To be more specific the problem is that in qiime's fast_unifrac.py in function delete_test() (in my case line 176) all branches are deleted because node.Name() returns the OTU names with quotes but the OTU table has them without, i.e., they don't match with the keys in the dicitonary env.
Cheers,
Lowry