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), pedigree.txt (sample input pedigree file), and pedmine.out, ids_subset.out, and kin_subset.out (sample output files).

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.