Published July 7, 2020 | Version v1
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LDhat coalescent likelihood lookup table for 320 sequences with theta = 0.01

  • 1. Rutgers University


The LDhat `complete` tool uses the method of Fearnhead and Donnelly (2001) to calculate coalescent likelihoods (via importance sampling) for all possible two-locus haplotype configurations for a given number of sequences for a grid of recombination rate (rho) values. See the LDhat documentation. We considered the case of 320 sequences, for which there are 708400 configurations.

Generating this table was computationally expensive (approximately 60,000 CPU hours), hence the interest in sharing it for reuse. The included sbatch job script illustrates how the computations were done (with GNU Parallel). The script could be adapted to compute a similar table on Linux clusters that use Slurm for cluster management/job scheduling.


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Is supplement to
Journal article: 10.1128/JVI.00541-21 (DOI)


PIRE: U.S.-East Africa Research and Education Partnership: Cassava mosaic disease - A paradigm for the evolution of insect-transmitted plant virus pathosystems 1545553
National Science Foundation