Efficient pedigree recording for fast population genetics simulation
, , , and .
PLOS Computational Biology 14 (11): 1-21 (November 2018)

Author summary Sexually reproducing organisms are related to the others in their species by the complex web of parent-offspring relationships that constitute the pedigree. In this paper, we describe a way to record all of these relationships, as well as how genetic material is passed down through the pedigree, during a forwards-time population genetic simulation. To make effective use of this information, we describe both efficient storage methods for this embellished pedigree as well as a way to remove all information that is irrelevant to the genetic history of a given set of individuals, which dramatically reduces the required amount of storage space. Storing this information allows us to produce whole-genome sequence from simulations of large populations in which we have not explicitly recorded new genomic mutations; we find that this results in computational run times of up to 50 times faster than simulations forced to explicitly carry along that information.
  • @peter.ralph
This publication has not been reviewed yet.

rating distribution
average user rating0.0 out of 5.0 based on 0 reviews
    Please log in to take part in the discussion (add own reviews or comments).