Alejandro A. Schäffer
Rice University
This document is meant to accompany FASTLINK, version 2.0 and beyond. It describes some aspects of pedigree loops in FASTLINK. This material is based on pages 170-171 of Analysis of Human Genetic Linkage by Ott, Section 2.8 of Linkage Analysis Package II: User's Guide To Programs, and Section 4 of ``Avoiding Recomputation in Linkage Analysis'' by A. A. Schäffer, S. K. Gupta, K. Shriram, and R. W. Cottingham Jr. (this is paper2.ps that comes with the FASTLINK distribution starting at version 2.0). It differs from these sources in that the presentation here is more comprehensive and more colloquial in nature. Thanks to Brian Nichols (U. Iowa) for asking enough questions about loops to motivate me to write this document. Thanks to Sandeep Gupta (Rice University) for helpful comments on my first draft. Unless otherwise noted, comments apply both to LINKAGE and FASTLINK.