Tag: QTL

QMSIM 1.10 – Qtl and Marker SIMulator

QMSIM 1.10

:: DESCRIPTION

QMSim (Qtl and Marker SIMulator) was designed to simulate a wide range of genetic architectures and population structures in livestock. Large scale genotyping data and complex pedigrees can be efficiently simulated. QMSim is a family based simulator, which can also take into account predefined evolutionary features, such as LD, mutation, bottlenecks and expansions. The simulation is basically carried out in two steps: In the first step, a historical population is simulated to establish mutation-drift equilibrium and, in the second step, recent population structures are generated, which can be complex. QMSim allows for a wide range of parameters to be incorporated in the simulation models in order to produce appropriate simulated data.

::DEVELOPER

Mehdi Sargolzaei , Flavio Schenkel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 QMSim

:: MORE INFORMATION

Citation

Sargolzaei, M. and F. S. Schenkel. 2009.
QMSim: a large-scale genome simulator for livestock.
Bioinformatics, 25: 680-681. doi:10.1093 /bioinformatics/btp045

QTLNETWORK 2.1 – Map QTL with Epistatic and QE interaction effects in Experimental Populations

QTLNETWORK 2.1

:: DESCRIPTION

QTLNetwork is a software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines.

::DEVELOPER

ZJU-IBI

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX

:: DOWNLOAD

 QTLNETWORK

:: MORE INFORMATION

Citation

Yang, Hu, Hu, Yu, Xia, Ye, Zhu (2008),
“QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations“,
Bioinformatics. 24(5):721-723.

SPSSQTL 1.0 – Statistical Power and Sample Size for QTL Detection

SPSSQTL 1.0

:: DESCRIPTION

SPSSQTL (Statistical Power and Sample Size for QTL Detection) is a computer program for calculating statistical power and sample size for detecting QTL and candidate gene effects, including single-locus effects and pairwise epistasis effects.

::DEVELOPER

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

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 SPSSQTL

:: MORE INFORMATION

QTL-GPR – QTL Mapping with Count Trait

QTL-GPR

:: DESCRIPTION

QTL-GPR (quantitative trait loci – Generalized Poisson Regression) is a Matlab code for QTL mapping with count trait.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

 QTL-GPR

:: MORE INFORMATION

Citation:

Genetics. 2006 Dec;174(4):2159-72. Epub 2006 Oct 8.
On the generalized poisson regression mixture model for mapping quantitative trait loci with count data.
Cui Y1, Kim DY, Zhu J.

R/qtl 1.48-1 – QTL Mapping Environment

R/qtl 1.48-1

:: DESCRIPTION

R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses. It is implemented as an add-on package for the freely available and widely used statistical language/software R

::DEVELOPER

R/qtl team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 R/qtl

:: MORE INFORMATION

Citation

Broman KW, Wu H, Sen Ś, Churchill GA (2003)
R/qtl: QTL mapping in experimental crosses.
Bioinformatics (2003) 19 (7): 889-890.

BioMercator v4.2.3 – Genetic Maps and QTL Integration

BioMercator v4.2.3

:: DESCRIPTION

BioMercator is a standalone application for: (1) Displaying genetic maps and QTL through a graphical user interface. (2) Performing automatic compilations of several genetic maps through a projection process. (3) Computing meta-analysis of QTL detected in independent experiments.

:: DEVELOPER

ABI Bioinformatic and Informatic Team 

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 BioMercator

:: MORE INFORMATION

Citation:

Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J.
BioMercator: integrating genetic maps and QTL towards discovery of candidate genes.
Bioinformatics. (2004) Sep 22;20(14):2321-6.

Olivier Sosnowski, Alain Charcosset and Johann Joets.
 BioMercator V3: an upgrade of genetic map compilation and QTL meta-analysis algorithms
Bioinformatics. 2012 Aug 1;28(15):2082-3. doi: 10.1093/bioinformatics/bts313.

FastQTL 2.184 – Fast and Efficient QTL mapper for thousands of Molecular Phenotypes

FastQTL 2.184

:: DESCRIPTION

FastQTL is a method that implements a popular cis-QTL mapping strategy in a user- and cluster-friendly tool.

::DEVELOPER

FunPopGen lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 FastQTL

:: MORE INFORMATION

Citation

Fast and efficient QTL mapper for thousands of molecular phenotypes.
Ongen H, Buil A, Brown AA, Dermitzakis ET, Delaneau O.
Bioinformatics. 2015 Dec 26. pii: btv722.

Rice Gene Thresher 2.0 – Mining Genes underlying QTL in Rice Genome

RiceGeneThresher 2.0

:: DESCRIPTION

RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions.

::DEVELOPER

Rice Gene Discovery Unit, Kasetsart University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jan;37(Database issue):D996-1000. doi: 10.1093/nar/gkn638.
RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.
Thongjuea S, Ruanjaichon V, Bruskiewich R, Vanavichit A.

PLABQTL 20100816 – computer program to Map QTL

PLABQTL 20100816

:: DESCRIPTION

PLABQTL (PLAnt Breeding QTL analysis)is a program written for the detection of loci which affect the variation of quantitative traits. Its main purpose is to localize and characterize QTL (Quantitative
Trait Loci).

::DEVELOPER

H. Friedrich Utz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • windows

:: DOWNLOAD

PLABQTL

:: MORE INFORMATION

Citation

Utz and Melchinger, 1996:
PLABQTL: A program for composite interval mapping of QTL.
Journal of Agricultural Genomics 2, 1-5

QTLBIM 2.0.7 – QTL Bayesian Interval Mapping

QTLBIM 2.0.7

:: DESCRIPTION

QTLBIM (QTL Bayesian Interval Mapping), provides a Bayesian model selection approach to map multiple interacting QTL. It works on experimentally inbred lines and performs a genome-wide search to locate multiple potential QTL. The package can handle continuous, binary and ordinal traits.

::DEVELOPER

QTLBIM Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 QTLBIM

:: MORE INFORMATION

Citation:

Yandell BS, Mehta T, Banerjee S, Shriner D, Venkataraman R, Moon JY, Neely WW, Wu H, von Smith R, Yi N.
R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses.
Bioinformatics. 2007 Mar 1;23(5):641-3. Epub 2007 Jan 19.