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Allegro, a new computer program for multipoint linkage analysis

Nature Genetics volume 25, pages 12–13 (2000)Cite this article

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We have developed several improvements to the computational algorithms of Genehunter. The new algorithms have been incorporated in a computer program for multipoint linkage analysis, Allegro, which is available free for non-commercial use (allegro@decode.is). Included is a program manual, a technical report and the source code. Like Genehunter, Allegro uses a hidden Markov model9,10,11, and time and memory costs still grow exponentially with pedigree size, but it is considerably faster than Genehunter (typically 20–100 times, Table 1). Apart from allowing for larger pedigrees (typically 20–30% larger), the speed improvement is relevant for simulation studies. Instead of providing the technical details of the computational algorithms, here we describe Allegro from the user's perspective.

Table 1 Run times for Genehunter (version 1.3) and Allegro
Full size table

Allegro has much of the functionality of Genehunter and Genehunter-Plus. Specifically, Allegro calculates multipoint parametric lod scores, NPL scores and allele-sharing lod scores based on the scoring functions Spairs and Sall (ref. 12), reconstruction of haplotypes, estimated recombination count between markers (observed map), and entropy information. The X chromosome is supported in all calculations. Although planned for the future, Allegro currently does not support quantitative traits.

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Figure 1: Pedigrees used in timing experiments.

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Acknowledgements

We thank the statistics group at Decode Genetics, D. Nicolae and H. Cordell for extensive testing of Allegro and suggestions.

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Authors and Affiliations

  1. Decode Genetics, Lynghals 1, Reykjavik, 110, Iceland

    Daniel F. Gudbjartsson, Kristjan Jonasson, Michael L. Frigge & Augustine Kong

  2. Institute of Statistics and Decision Sciences, Duke University, Durham, North Carolina, USA

    Daniel F. Gudbjartsson

  3. Department of Human Genetics, University of Chicago, Chicago, Illinois, USA

    Augustine Kong

Authors
  1. Daniel F. Gudbjartsson
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  2. Kristjan Jonasson
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  3. Michael L. Frigge
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  4. Augustine Kong
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Correspondence to Daniel F. Gudbjartsson.

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Gudbjartsson, D., Jonasson, K., Frigge, M. et al. Allegro, a new computer program for multipoint linkage analysis. Nat Genet 25, 12–13 (2000). https://doi.org/10.1038/75514

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