Pure Parsimony Xor Haplotyping

  • Paola Bonizzoni
  • Gianluca Della Vedova
  • Riccardo Dondi
  • Yuri Pirola
  • Romeo Rizzi
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5542)


The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies [1]. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without identifying the homozygous alleles. In this paper we propose a formulation based on a well known model used in haplotype inference: pure parsimony. We exhibit exact solutions of the problem by providing polynomial-time algorithms for some restricted cases and a fixed-parameter algorithm for the general case. These results are based on some interesting combinatorial properties of a graph representation of the solutions. Moreover we propose a heuristic and produce an experimental analysis showing that it scales to real-world instances taken from the HapMap project.


Gray Code Auxiliary Graph Graph Realization Perfect Phylogeny Genotype Matrix 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Paola Bonizzoni
    • 1
  • Gianluca Della Vedova
    • 2
  • Riccardo Dondi
    • 3
  • Yuri Pirola
    • 1
  • Romeo Rizzi
    • 4
  1. 1.DISCoUniv. Milano-BicoccaItaly
  2. 2.Dip. StatisticaUniv. Milano-BicoccaItaly
  3. 3.Dip. Scienze dei Linguaggi, della Comunicazione e degli Studi CulturaliUniv. BergamoItaly
  4. 4.DIMIUniv. UdineItaly

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