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    • RcppTskit

      Public
      R access to the tskit C API
      C
      53221Updated Apr 10, 2026Apr 10, 2026
    • AlphaSimR

      Public
      R package for breeding program simulations
      R
      Other
      270140Updated Apr 3, 2026Apr 3, 2026
    • R
      Other
      0110Updated Mar 2, 2026Mar 2, 2026
    • AlphaPeel

      Public
      AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees
      Python
      MIT License
      12000Updated Feb 27, 2026Feb 27, 2026
    • Formatting genetic map (recombination rate map) for pig species in stdpopsim
      Jupyter Notebook
      1000Updated Feb 25, 2026Feb 25, 2026
    • tinyhouse

      Public
      tinyhouse: Internal (house) functions used across many AlphaGenes tools
      Python
      7000Updated Feb 5, 2026Feb 5, 2026
    • R universe for packages from the HighlanderLab and friends
      0000Updated Feb 4, 2026Feb 4, 2026
    • Scripts for spatial modelling of the ADGG data
      R
      0000Updated Jan 24, 2026Jan 24, 2026
    • This is a repository hosting public information about the EUCARPIA 2025 Biometrics in Plant Breeding in Edinburgh 17-19th September 2025 + Satellite workshop 15…
      Ruby
      2500Updated Jan 5, 2026Jan 5, 2026
    • Accounting for nuclear - and mito-genome in dairy cattle breeding: a simulation study
      R
      0210Updated Dec 9, 2025Dec 9, 2025
    • AlphaImpute2: pedigree- and population-based genotype imputation
      Python
      MIT License
      9000Updated Dec 4, 2025Dec 4, 2025
    • SIMplyBee

      Public
      SIMplyBee R package extends AlphaSimR for simulating honeybee populations and breeding programmes
      R
      Other
      63621Updated Nov 20, 2025Nov 20, 2025
    • Code to convert ASR simulations to k-mer datasets
      R
      MIT License
      0000Updated Nov 6, 2025Nov 6, 2025
    • Principal Component Analysis of Pedigree Relationship Matrix via Randomized SVD
      Jupyter Notebook
      56100Updated Oct 10, 2025Oct 10, 2025
    • Script for the simulation reported on paper ... DOI:
      R
      2000Updated Oct 6, 2025Oct 6, 2025
    • Scripts for quantitative genetic analyses leveraging genome sequence context
      R
      GNU General Public License v3.0
      1200Updated Sep 9, 2025Sep 9, 2025
    • Project on evaluating the estimation of inbreeding load in dairy sheep and selecting against it
      R
      1000Updated Sep 5, 2025Sep 5, 2025
    • almondsim

      Public
      Almond breeding simulations with AlphaSimR
      R
      Other
      19000Updated Aug 25, 2025Aug 25, 2025
    • This repository contain R scripts that TODO
      R
      1010Updated Aug 22, 2025Aug 22, 2025
    • Simulation of honeybee imports by Irene de Carlos
      R
      0000Updated Apr 23, 2025Apr 23, 2025
    • Fortran
      MIT License
      2000Updated Apr 2, 2025Apr 2, 2025
    • vpapin_pine_gs

      Public archive
      Simulation of genomic prediction in maritime pine and factors affecting its accuracy
      R
      1200Updated Mar 7, 2025Mar 7, 2025
    • AlphaPart

      Public
      AlphaPart implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes
      R
      4000Updated Feb 23, 2025Feb 23, 2025
    • R
      1000Updated Feb 20, 2025Feb 20, 2025
    • Plant breeding simulations with AlphaSimR
      HTML
      Other
      192710Updated Jan 5, 2025Jan 5, 2025
    • Scripts for genomic prediction and association studies using tree sequence in rice
      R
      0000Updated Dec 13, 2024Dec 13, 2024
    • Python
      MIT License
      2100Updated Nov 15, 2024Nov 15, 2024
    • Analysis of the effect of mtDNA on dairy cattle performance
      R
      MIT License
      0100Updated Oct 28, 2024Oct 28, 2024
    • HTML
      MIT License
      1000Updated Sep 9, 2024Sep 9, 2024
    • Pipeline to infer tree sequences with different datasets
      Python
      MIT License
      73151Updated Jul 26, 2024Jul 26, 2024
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