Home of Quantitative Genetics Software from Vinzent Boerner
- For scientific use all executables come free of charge but users must acknowledge the author.
- Commerical users must obtain a license.
- All executables are optimized for 64 bit Intel architecture, for Linux only, and run from the command line
- A Linux kernel >= 3.10 is required
- Stack size must be set to unlimited. Execute "ulimit -s unlimited" on your command line or adjust your .bashrc
- Many implemented algorithms are parallelized or make use of Intel's parallelized Math Kernel library
- Users may set the number of threads with the environment variables "OMP_THREAD_LIMIT", "OMP_NUM_THREADS" and "MKL_NUM_THREADS"
- For software versions specifically designed for single core computers please contact the author
- For question, comments and bug reports email to: mail me
- Contact: mail me
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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
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| Executable |
Manual |
Examples |
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Literature: Boerner and Tier Genet Sel Evol (2016) 48:63,DOI 10.1186/s12711-016-0241-x
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ParentSearch
A software for large scale SNP marker based parentage assignment and verfication
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| Executable |
Manual: --help |
Example:comming soon |
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Literature: Boerner Genet Sel Evol (2017) 49:50, DOI 10.1186/s12711-017-0324-3
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BreedComp
A software for large scale SNP marker based estimation of the composition of admixed SNP genotypes
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| Executable |
Manual: --help |
Example:comming soon |
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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
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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
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| 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).
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| 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.