HighlanderLab's repositories
jbancic_alphasimr_plants
Plant breeding simulations with AlphaSimR
jbancic_GEIsim
This repository contains examples of code for simulating genotype by environment interaction
tree_seq_pipeline
Pipeline to infer tree sequences with different datasets
gmafrafortuna_mtdna_breed
Accounting for nuclear - and mito-genome in dairy cattle breeding: a simulation study
nlubanga_tea_breeding_gs
Simulation of tea breeding programmes using genomic selection
EUCARPIA2025BiometricsPlantBreeding
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
gdejong_gca_with_dominance_models
Simulation scripts from the study of Guilherme de Jong about genomic prediction with additive and dominance effects in maize breeding
ipocrnic_Layer_OCS
Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study
vbrajkovic_cattle_mtdna
Analysis of the effect of mtDNA on dairy cattle performance
AlphaPart
AlphaPart implements a method for partitioning genetic trends to quantify the sources of genetic gain in breeding programmes
AlphaSimR
R package for breeding program simulations
rbsmith_bsf_paternity
Simulation by RB Smith for evaluating the number of fathers in black soldier flies
toliveira_alphapart_variance
A method for partitioning trends in genetic mean and variance to understand breeding practices
AlphaImpute2
AlphaImpute2: pedigree- and population-based genotype imputation
AlphaPeel
AlphaPeel: calling, phasing, and imputing genotype and sequence data in pedigrees
AlphaPlantImpute2
AlphaPlantImpute2: Genotype imputation for plant populations
ipocrnic_OptimisedCore4APY
Optimisation of the core subset for the APY approximation of genomic relationships
lstrachan_honeybee_relatedness
This repository contain R scripts that demonstrates the principles of expected and realised genetic relatedness among individual honeybees using SIMplyBee.
PedigreeToolsF90
PedigreeTools.f90 is pedigree cleaning protocol made up of several programmes
tinyhouse
tinyhouse: Internal (house) functions used across many AlphaGenes tools
toliveira_graphical_ped
Pedigree based mixed-effects models using directed acyclic graphs
vpapin_pine_gs
Simulation of genomic prediction in maritime pine and factors affecting its accuracy
yma_bsf_pop_diff_pool_seq
Scripts for population genetic differentiation of black soldier fly via pool sequencing