Tag: Quantitative Trait

AutocorQ – Characterise and Test the Spatial Autocorrelation of Quantitative Traits

AutocorQ

:: DESCRIPTION

AutocorQ is a simple software to characterise and test the spatial autocorrelation of quantitative traits. It computes Moran’s I statistics, can provide pairwise autocorrelation coefficient between individuals, and computes the slope of the linear regression of these coefficients on the spatial distance or its logarithm. The significance of the coefficients is assessed by random permutation tests.

::DEVELOPER

Olivier Hardy @ Evolutionary Biology & Ecology, Université Libre de Bruxelles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  AutocorQ

:: MORE INFORMATION

LSKM 1.0 – Multilocus Association Test for Quantitative Traits

LSKM 1.0

:: DESCRIPTION

LSKM consists of a R routine that allow for semiparametric association testing of quantitative traits with multiple SNP predictors, adjusting for environmental covariates.

::DEVELOPER

Epstein software

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LSKM

:: MORE INFORMATION

Citation

Kwee et al. (2008)
A Powerful and Flexible Multilocus Association Test for Quantitative Traits
Am J Hum Genet 82: 386-397

GADS 1.1 – Parametric Linkage Analysis of Quantitative Traits

GADS 1.1

:: DESCRIPTION

GADS is aoftware for Genetic Analyses of quantitative traits Distributed with Spike on the base of large pedigrees without loops

::DEVELOPER

Group of the Methods of Genetic Analysis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Perl
  • Python

:: DOWNLOAD

 GADS

:: MORE INFORMATION

Citation:

GADS software for parametric linkage analysis of quantitative traits distributed as a point-mass mixture.
Axenovich TI, Zorkoltseva IV.
Comput Biol Chem. 2012 Feb;36:13-4. doi: 10.1016/j.compbiolchem.2011.11.004.

QTL Cartographer 1.17 / Windows QTL Cartographer 2.5.011 – Map Quantitative Traits

QTL Cartographer 1.17 / Windows QTL Cartographer 2.5.011

:: DESCRIPTION

QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers.

Windows QTL Cartographer maps quantitative trait loci in cross populations from inbred lines. It incorporates many of the modules found in its command-line sibling, QTL Cartographer (see above). WinQTLCart includes powerful graphic tools for presenting mapping results and can import and export data in a variety of formats.

::DEVELOPER

Shengchu Wang, Christopher J. Basten and Zhao-Bang Zeng

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Perl

:: DOWNLOAD

 QTL Cartographer , Windows QTL Cartographer 

:: MORE INFORMATION

quantiNEMO 1.0.4 – Simulate Quantitative Traits with Explicit Genetic Architecture

quantiNEMO 1.0.4

:: DESCRIPTION

quantiNEMO is an individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population. quantiNEMO was developed to investigate the effects of selection, mutation, recombination, and drift on quantitative traits with varying architectures in structured populations connected by migration and located in a heterogeneous habitat. quantiNEMO is highly flexible at various levels: population, selection, trait(s) architecture, genetic map for QTL and/or markers, environment, demography, mating system, etc.

::DEVELOPER

Samuel Neuenschwander, Jérôme Goudet, Frédéric Hospital, andFrédéric Guillaume.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

quantiNEMO

:: MORE INFORMATION

Citation

Neuenschwander S, Hospital F, Guillaume F, Goudet J (2008)
quantiNEMO: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation
Bioinformatics 24, 1552-1553.

MQscore 1.0 / MQscore_SNP 1.1 – Parametric Linkage analysis of Quantitative Traits in large pedigrees

MQscore 1.0

:: DESCRIPTION

MQscore is a program which can be useful for parametric linkage analysis of quantitative traits on the base of large pedigrees without loops.

MQscore_SNP is a program for multipoint parametric linkage analysis of quantitative traits and SNP markers on the base of large pedigrees without loops.

::DEVELOPER

Laboratory of the Methods of Genetic Analysis , Institute of Cytology and Genetics, Novosibirsk, Russia.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl

:: DOWNLOAD

 MQscore , MQscore_SNP

:: MORE INFORMATION

Citation:

Ann Hum Genet. 2010 May;74(3):286-9.
MQScore_SNP software for multipoint parametric linkage analysis of quantitative traits in large pedigrees.
Axenovich TI, Aulchenko YS.

POLY 0.4.0 – Polygenic analysis and Power analysis of human Quantitative Traits

POLY 0.4.0

:: DESCRIPTION

POLY is a computer program for polygenic analysis and power analysis of human quantitative traits. It is convenient to use POLY to analyze multiple models / traits in large pedigrees

:DEVELOPER

Wei-Min Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • C++ Compiler
:: DOWNLOAD

 POLY

:: MORE INFORMATION

Citation

Genet Epidemiol. 2006 Sep;30(6):471-84.
Estimating the power of variance component linkage analysis in large pedigrees.
Chen WM, Abecasis GR.

XWXW – Linkage Analysis of Quantitative Traits

XWXW

:: DESCRIPTION

XWXW implements the Unified Haseman-Elston method for non-parametric linkage test with quantitative traits. It optimally utilizes the information from a sib-pair. It is uniformly more powerful than both the classical H-E method and the revistited H-E method. Program GENIBD from SAGE or GeneHunter2 is required for sib-pair ibd estimation.

::DEVELOPER

FBAT-Toolkit Team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux/ Sunsparc stations

:: DOWNLOAD

XWXW

:: MORE INFORMATION

References

Xu X, Palmer LJ, Horvath S, and Wei LJ.  Combining Multiple Phenotypic Traits Optimally for Detecting Linkage with Sib-pair Observations. (2001) Genet. Epidemiol.

Xu X., Weiss S. Xu X., Wei LJ. A unified Haseman-Elston regression method for testing linkage with quantitative trait (2000) Am. J. Hum. Genet. 67: 1025-8