Haplotype-Based Tracking of Admixed Population for Breed Composition Estimation

Simulate populations and track haplotypes over generations to evaluate population admixture. The 'HAPTRACE' supports customisable population parameters, including size, number of markers, mutation rates and recombination.

HAPTRACE

Haplotype-Based Tracking of Admixed Population for Breed Composition Estimation (HAPTRACE) is an open-source R package which simulates and tracks haplotype in an admixed population for accurate estimation of breed composition. This package offers multiple functionalities including estimation of true breed composition, visualization of haplotypes of admixed animals, simulation of purebred and admixed animals with tracked haplotype, genotype and phenotype.

Installation

The github repository contains the recent version of HAPTRACE (0.1.2). You can install the development version of HAPTRACE from GitHub with:

#install.packages("remotes")
remotes::install_github("shwetasahoo12/HAPTRACE", build_vignettes = TRUE)

Example

To see the example simulation of the package, refer to the vignette below:

## Example simulation
library(HAPTRACE)
vignette("Introduction_HAPTRACE")

Citation

If you use this package in your research, please cite it as:

Sahoo S, Ferdosi M, van der Werf J, de las Heras-Saldana S (2025). “Proc. Assoc. Advmt. Anim. Breed. Genet.” Proc. Assoc. Advmt. Anim. Breed. Genet., 26, 323.