I’ve been trying out weighted and unweighted UniFrac on the AbRecovery dataset and have been getting some strange results with the latest release (1.13.0). I loaded the abrecovery.paup.nj tree and ran the unifrac.unweighted() command. Using the default settings, mothur came up with a UWScore that was pretty close (0.703848) to the value given in the tutorial (0.6818) and a significance score of zero. I ran it again setting random=true to see if the significance matched. After cranking through the 1,000 iterations, the output showed up as:
Tree# Groups UWScore UWSig
1 A-B 0.715765 1
1 A-C 0.726746 1
1 B-C 0.75528 1
Opening the abrecovery.paup.nj.unweighted file shows no iterations, just the same three lines shown in the output above. I’ve run unweighted.unifrac() on a number of my own trees with the same results: normal looking score but always a significance score of 1. Any ideas?
Conversely, unifrac.weighted seems to be working fine.