This is an old script that predates the current (fast) version of corMLPE. The method implemented in this script is slow and will balk at a large number of pairwise comparisons. Still, it may be of some use, as it can handle missing comparisons (whereas the current version cannot.)
Direct questions/comments/complaints to [email protected]. I don't really use this script anymore, but may be able to help if it doesn't work for your particular use case.