The software FamLink provides functions for likelihood calculation for family relationships/pedigrees using linked DNA marker data. FamLink is released as a freeware without any strings attached. The software provides an easy-to-use graphical user interface which allows for linkage calculation based on efficient implementation of and IBD algorithm.
FamLink is developed and maintained by Daniel
Kling at National Board of Forensic Medicine, Sweden, together with Thore Egeland at Norwegian Institute of Life Sciences,
Norway, and Andreas Tillmar at National Board of Forensic Medicine, Sweden.
See further contact details here.
The software provides an easy-to-use graphical user interface, which allows for linkage calculation based on the Lander-Green algorithm. Previous versions of FamLink relied solely on the Merlin engine (Abecasis et al., Nat. Genet., 2002) for numerical calculations. Merlin is based on the Lander-Green algorithm which scales computationally linear in the number of markers, but not in the complexity of the pedigree. However, we have found that fairly complex pedigrees can be handled and we have not encountered practical cases where computation time has been a serious problem. In fact, FamLink improves on software we are familiar with (such as Familias) when it comes to computation time and dealing with inbreeding and marriage loops.
Recent extension, version 2.2 and above, implements a completely new
algorithm/model for likelihood computations. The model is based on similar
concepts as the Lander-Green algorithm with inheritance vectors and IBD codes.
In addition our algorithm models genotype uncertainty through a model for
genotype likelihoods, detailed in Mostad et al. In
addition, the model accounts for subpopulation structure through the fixation
parameter (Fst/theta). We expect to include more
information and examples on our new algorithm soon.
Kling, D., Egeland, T., & Tillmar, A. O. (2012). FamLink–a user friendly software for linkage calculations in family genetics. Forensic Science International: Genetics, 6(5), 616-620.
Kling, D., Tillmar, A., Egeland, T., & Mostad, P. (2015). A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations. International journal of legal medicine, 129, 943-954.
Mostad, P., Tillmar, A., & Kling, D. (2023). Improved computations for relationship inference using low-coverage sequencing data. BMC bioinformatics, 24(1), 90.
Last updated August, 2023
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