GSdesign 0.2 – Breeding program Design with Genomic Selection

GSdesign 0.2

:: DESCRIPTION

GSdesign optimizes breeding programs for maximum genetic gain.

::DEVELOPER

Endelman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 GSdesign

:: MORE INFORMATION

Citation

Jeffrey B. Endelman, Gary N. Atlin, Yoseph Beyene, Kassa Semagn, Xuecai Zhang, Mark E. Sorrells and Jean-Luc Jannink
Optimal Design of Preliminary Yield Trials with Genome-Wide Markers
Crop Science Vol. 54 No. 1, p. 48-59,doi:10.2135/cropsci2013.03.0154

rrBLUP 4.6.1 – Ridge Regression and other kernels for Genomic Selection

rrBLUP 4.6.1

:: DESCRIPTION

rrBLUP is an R package for genomic selection and association mapping.

::DEVELOPER

Endelman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

 rrBLUP

:: MORE INFORMATION

Citation

Jeffrey B. Endelman
Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP
The Plant Genome Vol. 4 No. 3, p. 250-255 doi:10.3835/plantgenome2011.08.0024

AlphaBayes – Performing Genome Wide Association Studies and Genomic Selection

AlphaBayes

:: DESCRIPTION

AlphaBayes is a software package for carrying out genome wide association studies and genomic selection. It implements several Bayesian models and can simultaneously or separately fit SNPs, fixed effects, polygenic, and genetic group effects.

::DEVELOPER

John Hickey

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 AlphaBayes

:: MORE INFORMATION

BLUP_GEN / BLUP_SNP – Estimate Solutions for Genomic Selection Models

BLUP_GEN / BLUP_SNP

:: DESCRIPTION

BLUP_GEN and BLUP_SNP are (Fortran90) programs to estimate solutions for genomic selection models, parameterized in terms of genomic relationship matrices or SNP effects. The programs accept heterogeneous variances as is often the case if pre-corrected phenotypes (DYD’s) are used

blup_snp computes solutions for snp effects considering them as random, with a common variance.

Blup_gen solves an equivalent system of equations based on G, the matrix of covariances among individuals.

::DEVELOPER

Andrés Legarra , andres dot legarra at toulouse point inra punto fr , Anne Ricard, Olivier Filangi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Fortran90

:: DOWNLOAD

 BLUP_GEN / BLUP_SNP

:: MORE INFORMATION

GS3 2.2.3 – Estimates Fixed and Random Effects, Breeding Values and SNP effects for Genomic Selection

GS3 2.2.3

:: DESCRIPTION

GS3 (Genomic Selection / Gibbs Sampling / Gauss Seidel) is a program that estimates fixed and random effects, breeding values and SNP effects for genomic selection. It includes normal, mixture, or double exponential distributions for SNP effects, i.e. GBLUP, the so-called BayesCPi, and the Bayesian Lasso. It allows estimation of the variances and effects of SNPs, polygenic and environmental effects, and also the inclusion of heterogeneous variances as for the analysis of DYD’s

::DEVELOPER

Andrés Legarra , andres dot legarra at toulouse point inra punto fr , Anne Ricard, Olivier Filangi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 GS3

:: MORE INFORMATION

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