a question about the "LIBSHUFF"

Here i want to know whether the differences among the 3 clone librarys (x,y,z)are significant.I have conducted the "LIBSHUFF"command with the default setting by mothur, and got two fills named ".summary"and “.coverage”.From the summary file, i got the results of significance.However,i also want to draw figures about results of selected LIBSHUFF comparisons of clones from x to y,y to z,and z to x. The coverge file provide date of 3 valuesof “Cx” and 6 values of “Cxy”,and Cx is “homologous” coverge, "Cxy"is the “heterologous” coverage. I caculated the (Cx-Cxy)2 by EXCEL.
Here the two questions are:
1.How to get the P-value shows in figure,or that is one of the walues shows in the summary file and which one shoud be?
2. In the figure, i need to draw broken lines which indicate the 950th value (or p=0.05)of (Cx-Cxy)2 for the randomized samples.where to get these date?

The p-value is calculated from randomized re-samplings of the data. So, you can’t calculate this by hand, which is what I think you’re asking in your first question. As for your second question, we do not provide this information. In part because I think it is a dangerous metric for people to use because doesn’t actually tell you anything.

Hope this helps,