GVCHAP 2.1 – Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers

GVCHAP 2.1

:: DESCRIPTION

GVCHAP is a computing pipeline for genomic prediction and variance component estimation using haplotypes and SNP markers.

::DEVELOPER

JOHN GARBE AND YANG DA , Department of Animal Science, University of Minnesota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

GVCHAP

:: MORE INFORMATION

Citation

Prakapenka D, Wang C, Liang Z, Bian C, Tan C, Da Y.
GVCHAP: A Computing Pipeline for Genomic Prediction and Variance Component Estimation Using Haplotypes and SNP Markers.
Front Genet. 2020 Apr 7;11:282. doi: 10.3389/fgene.2020.00282. PMID: 32318093; PMCID: PMC7154123.

GVCBLUP 3.9 / GVCeasy 1.3 – Genomic Prediction and Variance Component Estimation

GVCBLUP 3.9 / GVCeasy 1.3

:: DESCRIPTION

GVCBLUP is a computer package for genomic prediction and variance component estimation for additive and dominance effects using SNP markers.

GVCeasy is the graphical user interface for the GVCBLUP package.

::DEVELOPER

The authors of GVCBLUP:
Chunkao Wang, Dzianis Prakapenka, Shengwen Wang,
H. Birali Runesha and Yang Da

The authors of GVCeasy:
Sujata Pulugurta, Chunkao Wang, Dzianis Prakapenka,
H. Birali Runesha, Yang Da

, Department of Animal Science, University of Minnesota

:: SCREENSHOTS

GVCeasy

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

GVCBLUP  , GVCeasy

:: MORE INFORMATION

Citation

Da Y, Wang C, Wang S, Hu G (2014)
Mixed Model Methods for Genomic Prediction and Variance Component Estimation of Additive and Dominance Effects Using SNP Markers.
PLoS ONE 9(1): e87666. doi:10.1371/journal.pone.0087666.

DAIRRy-BLUP 0.1 – High Performance Computing approach to Genomic Prediction

DAIRRy-BLUP 0.1

:: DESCRIPTION

DAIRRy-BLUP is a Distributed AI-REML Ridge Regression Best Linear Unbiased Prediction framework for genomic prediction.

::DEVELOPER

Arne De Coninck

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MPI
  • ScaLAPACK and all its dependencies BLAS, BLACS, LAPACK, PBLAS
  • HDF5
  • CMake

:: DOWNLOAD

 DAIRRy-BLUP

:: MORE INFORMATION

Citation:

DAIRRy-BLUP: a high-performance computing approach to genomic prediction.
De Coninck A, Fostier J, Maenhout S, De Baets B.
Genetics. 2014 Jul;197(3):813-22. doi: 10.1534/genetics.114.163683