PedMine 1.0.0 is a Java program that uses an optimization algorithm (simulated annealing) to identify a subset of maximally unrelated individuals from one or more pedigrees based on pair-wise kinship coefficients.  PedMine was specifically designed for use in the context of family-based genetic studies in population isolates, where all individuals are often detectably related to one another (e.g., see figure below).  PedMine was programmed by Conner Sandefur, a graduate student in the lab of Julie Douglas.

The PedMine package (pedmine.zip) includes pedmine.jar (program executable), pedmine.java (source code), pedmine.pdf (documentation), and pedigree.txt (sample input pedigree file).

Use this citation in your publications:

Douglas JA, Sandefur CI (2008) PedMine – A simulated annealing algorithm to identify maximally unrelated individuals in population isolates, Version 1.0.0, February 5, 2008

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Download package

pedmine.zip

Figure.  Two distinct but related sibling pairs (filled circles) connect into a 229-member pedigree based on all known paths of recent, common ancestry.  Drawn using pfiddler version 0.5.  Black dots represent marriage nodes.