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Databases
Genotype
likelihoods Validation
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.
Download the software and use the getting started guide and the tutorial to start using FamLink.
If you need help in any way, please contact us.
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
You may send comments to daniel.kling@rmv.se