Tag: Variance Component

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.

iQTL-VC – iQTL mapping with Variance Component mode

iQTL-VC

:: DESCRIPTION

iQTL-VC is an R code for iQTL mapping with Variance Component model in experimental cross.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 iQTL-VC

:: MORE INFORMATION

Citation:

Li, G.X. and Y.H. Cui. (2010)
A general statistical framework for dissecting parent-of-origin effects underlying triploid endosperm traits in flowering plants.
Annals of Applied Statistics 4(3): 1214-1233.

BestRepeat 1.0 – Variance Components Linkage Analysis with Repeated Measurements

BestRepeat 1.0

:: DESCRIPTION

BestRepeat is a R package to calculate the optimal number of repeated measures for quantitative trait linkage analysis.

::DEVELOPER

Liming Liang

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BestRepeat

:: MORE INFORMATION

Citation

Liang L, Chen WM, Sham PC and Abecasis GR. (2009)
Variance Components Linkage Analysis with Repeated Measurements.
Human Heredity 67: 237-247.

TM 20110802 – Multiple Trait Estimation of Variance Components

TM 20110802

:: DESCRIPTION

TM (Threshold Model) is a (Fortran90) software for multiple trait estimation of variance components, breeding values and fixed effects in threshold, linear and censored linear models in animal breeding.  As of August, 2011 it has been modified to accept random seeds on input, and also to include user-defined covariance matrices among individuals (for instance, genomic relationship matrices).

::DEVELOPER

Andrés Legarra , andres dot legarra at toulouse point inra punto fr

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Fortran90

:: DOWNLOAD

 TM

:: MORE INFORMATION