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Individual based simulations of hybridizing populations, where the accumulation of junctions is tracked. Furthermore, mathematical equations are provided to verify simulation outcomes. Both simulations and mathematical equations are based on Janzen et al. (2018) and Janzen and Miro Pina (2022).
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Janzen, T. , Nolte, A. W. and Traulsen, A. (2018), The breakdown of genomic ancestry blocks in hybrid lineages given a finite number of recombination sites. Evolution, 72: 735-750. https://doi.org/10.1111/evo.13436
Lavretsky, P., Janzen, T. and McCracken, KG. (2019) Identifying hybrids & the genomics of hybridization: Mallards & American black ducks of Eastern North America. Ecology and Evolution 9: 3470-3490. https://doi.org/10.1002/ece3.4981
Janzen, T., & Miró Pina, V. (2022). Estimating the time since admixture from phased and unphased molecular data. Molecular Ecology Resources, 22, 908–926. https://doi.org/10.1111/1755-0998.13519
Version 2.1.2: Added Github website
Version 2.1.1: Fixed typo
in one of the examples
Version 2.1 : updated tbb multithreading
code, sped up tests, added NEWS file
Version 2.0 : merged many
functions with similar functionality, added vignette that provides
overview of all functionality.
Version 1.9 : added c++ versions
of the unphased and phased likelihoods.
Version 1.8 : added
multithreading using the TBB library.
Version 1.7 : Further
improved the recombination function following Hanno Hildenbrandt’s
suggestions
Version 1.6 : Improved the recombination function run
twice as fast
Version 1.5.1: Added option to track the true
number of junctions
Version 1.5 : Added simulation functions to
simulate phased an unphased data, including phasing error
Version
1.5 : Added support for inferring the time since admixture based on
phased and unphased data.
Version 1.4 : Added support for
estimating the number of junctions, and simulating the number of
junctions, under a backcrossing scheme, using the code supplied in
Lavretsky et al. 2019.
Version 1.3 : Added support for estimating
the time since admixture using unphased data.
Version 1.3 : Added
individual based simulations returning phased and unphased data.
Version 1.3 : Updated entire package to Roxygen.
Version 1.2 :
Added support for estimating the expected number of junctions for
arbitrarily distributed markers.
Version 1.1 : Updated random
number generation for picking recombination sites. Previous
implementation was limited to 6 digit precision, current precision is at
least double that, minimizing the probability of recombination occur
twice in the same location for an infinite chromosome.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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