Repositories list

• AlphaSimR

  Public
  R package for breeding program simulations

  R

  •

  Other

  •24•0•3•0•Updated Jan 3, 2026Jan 3, 2026

• tskitr

  Public
  R access to the tskit C API

  C

  •0•0•25•0•Updated Jan 2, 2026Jan 2, 2026

• gmafrafortuna_mtdna_breed

  Public
  Accounting for nuclear - and mito-genome in dairy cattle breeding: a simulation study

  R

  •0•2•1•0•Updated Dec 9, 2025Dec 9, 2025

• AlphaImpute2

  Public
  AlphaImpute2: pedigree- and population-based genotype imputation

  Python

  •

  MIT License

  •9•0•0•0•Updated Dec 4, 2025Dec 4, 2025

• SIMplyBee

  Public
  SIMplyBee R package extends AlphaSimR for simulating honeybee populations and breeding programmes

  R

  •

  Other

  •6•3•60•1•Updated Nov 20, 2025Nov 20, 2025

• hbecher_ASR2kmerGwas

  Public
  Code to convert ASR simulations to k-mer datasets

  R

  •

  MIT License

  •0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

• RandPedPCA

  Public
  Principal Component Analysis of Pedigree Relationship Matrix via Randomized SVD

  Jupyter Notebook

  •5•6•10•0•Updated Oct 10, 2025Oct 10, 2025

• amartin_born2guide_seq

  Public
  Script for the simulation reported on paper ... DOI:

  R

  •2•0•0•0•Updated Oct 6, 2025Oct 6, 2025

• EUCARPIA2025BiometricsPlantBreeding

  Public
  This is a repository hosting public information about the EUCARPIA 2025 Biometrics in Plant Breeding in Edinburgh 17-19th September 2025 + Satellite workshop 15-16th September

  Ruby

  •2•5•0•0•Updated Sep 25, 2025Sep 25, 2025

• gmafrafortuna_quangen_tree

  Public
  Scripts for quantitative genetic analyses leveraging genome sequence context

  R

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Sep 9, 2025Sep 9, 2025

• santonios_sheep_idl

  Public
  Project on evaluating the estimation of inbreeding load in dairy sheep and selecting against it

  R

  •1•0•0•0•Updated Sep 5, 2025Sep 5, 2025

• almondsim

  Public
  Almond breeding simulations with AlphaSimR

  R

  •

  Other

  •18•0•0•0•Updated Aug 25, 2025Aug 25, 2025

• lstrachan_patrilines

  Public
  This repository contain R scripts that TODO

  R

  •1•0•1•0•Updated Aug 22, 2025Aug 22, 2025

• ihouaga_adgg_spatial

  Public
  Scripts for spatial modelling of the ADGG data

  R

  •0•0•0•0•Updated Jul 8, 2025Jul 8, 2025

• idecarlos_honeybee_import

  Public
  Simulation of honeybee imports by Irene de Carlos

  R

  •0•0•0•0•Updated Apr 23, 2025Apr 23, 2025

• AlphaPhase

  Public
  Fortran

  •

  MIT License

  •2•0•0•0•Updated Apr 2, 2025Apr 2, 2025

• vpapin_pine_gs

  Public archive
  Simulation of genomic prediction in maritime pine and factors affecting its accuracy

  R

  •1•2•0•0•Updated 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

  •4•0•0•0•Updated Feb 23, 2025Feb 23, 2025

• svanvanhossou_africross

  Public
  R

  •1•0•0•0•Updated Feb 20, 2025Feb 20, 2025

• jbancic_alphasimr_plants

  Public
  Plant breeding simulations with AlphaSimR

  HTML

  •

  Other

  •18•25•1•0•Updated Jan 5, 2025Jan 5, 2025

• irebollo_rice_tree

  Public
  Scripts for genomic prediction and association studies using tree sequence in rice

  R

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• AlphaPeel

  Public
  AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees

  Roff

  •

  MIT License

  •12•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• AlphaFamImpute

  Public
  Python

  •

  MIT License

  •2•1•0•0•Updated Nov 15, 2024Nov 15, 2024

• vbrajkovic_cattle_mtdna

  Public
  Analysis of the effect of mtDNA on dairy cattle performance

  R

  •

  MIT License

  •0•1•0•0•Updated Oct 28, 2024Oct 28, 2024

• sheep_ts_demo

  Public
  HTML

  •

  MIT License

  •1•0•0•0•Updated Sep 9, 2024Sep 9, 2024

• tree_seq_pipeline

  Public
  Pipeline to infer tree sequences with different datasets

  Python

  •

  MIT License

  •7•3•15•1•Updated Jul 26, 2024Jul 26, 2024

• gdejong_gca_with_dominance_models

  Public archive
  Simulation scripts from the study of Guilherme de Jong about genomic prediction with additive and dominance effects in maize breeding

  R

  •1•1•0•0•Updated Jul 15, 2024Jul 15, 2024

• jbancic_GEIsim

  Public
  This repository contains examples of code for simulating genotype by environment interaction

  R

  •1•4•0•0•Updated Jul 15, 2024Jul 15, 2024

• lstrachan_honeybee_relatedness

  Public
  This repository contain R scripts that demonstrates the principles of expected and realised genetic relatedness among individual honeybees using SIMplyBee.

  R

  •0•0•0•0•Updated May 20, 2024May 20, 2024

• ipocrnic_OptimisedCore4APY

  Public archive
  Optimisation of the core subset for the APY approximation of genomic relationships

  R

  •

  MIT License

  •0•0•0•0•Updated Nov 22, 2023Nov 22, 2023