Home of Quantitative Genetics Software from Vinzent Boerner

BESSiE
A software for Best Linear Unbiased(BLUP) and Bayesian analysis of linear mixed models

  • Solves and Gibbs samples linear mixed models encompassing:
    • fixed factors
    • fixed covariables
    • random individual genetic factors
    • random maternal genetic factors
    • random environmental factos
    • random generic group factors
    • random SNP marker factors
  • Covers the full Bayesian alphabet
    • Bayes A
    • Bayes B
    • Bayes CPi
    • Bayes R
  • Acommmodates for all types of phenotypes
    • continuous
    • binary
    • categorical
Executable Manual Examples

Literature: Boerner and Tier Genet Sel Evol (2016) 48:63,DOI 10.1186/s12711-016-0241-x

ParentSearch
A software for large scale SNP marker based parentage assignment and verfication

Executable Manual: --help Example:comming soon

Literature: Boerner Genet Sel Evol (2017) 49:50, DOI 10.1186/s12711-017-0324-3

BreedComp
A software for large scale SNP marker based estimation of the composition of admixed SNP genotypes

Executable Manual: --help Example:comming soon

Literature: Vinzent Boerner and Doerte Wittenburg, On Estimation of Genome Composition in Genetically Admixed Individuals Using Constrained Genomic Regression, Frontiers in Genetics, 29/05/2018, doi: 10.3389/fgene.2018.00185

pedtool
A software for large scale pedigree manipulation and inference.

  • allows for normal pedigrees and probabilistic pedigrees (more than 2 parents per individual)
  • accommodates metafounders
  • builds numeric pedigrees from strings, sort them and find cyclic errors
  • reduces pedigrees to the desired number of individuals and generations
  • finds the independent blocks in the NRM and their members (thus allows to check whether genotypes provide linkage beyond pedigree)
  • calculates inbreeding coefficients, diagonal elements of the NRM, of the inverse NRM and Mendelian sampling terms
  • extracts blocks and bands from the NRM, generate the inverse NRM and its Cholesky factor
  • builds block A22 for single-step genetic analysis and if required inverts it
Executable Manual: --help Example:comming soon

sssadi
A multichain Single Side Gibbs Sampler for sampling Diagonal elements of the Inverse of large sparse matrices.

  • Samples diagonal and off-diagonal elements of the inverse of large sparse positive definite matrices (aka prediction error variances).
  • Runs many Gibbs chains in parallel.
  • Can accomodate for add-on dense blocks (e.g. in single step mixed model equation systems).
Executable Manual: --help Example:comming soon

Disclaimer: All software comes without any warranty and guaranteed support. It can be used by the scientific community free of charge. Commercial users must contact the authors.