Quantitative Trait Loci (QTL) Software
Many good software modules for statistical analysis of genomic data
are offered in the public domain. While many historically have been
created as standalone packages, very good tools are now available
on the free R platform.
[See Yandell's R Introduction for Biologists.]
Some
other packages use the commercial
MatLab environment.
Both R and MatLab are available on UNIX/Linux, Windows
(95/98/NT4/2000/ME on Intel-type machines),
and MacOS (7.6 or later for MatLab, 8.6 or later for R). Below are
some highlights. Follow links to find other modules and packages.
Return to Statistical Genomics References.
See QTL References for full
citations. This list includes some software explicitly for eQTL.
For more software, see Genetic Linkage Analysis.
- DIRECT
- least squares optimized code (fast)
- Ljungberg et al. (2002, 2003)
- eQTLViewer
- Expression QTL viewer
- Zou, Zeng (2007)
- JoinMap
- linkage maps for multiple crosses
- Stam (1993)
- MapManager/QTX
- complex trait analysis
- Meer, Cudmore, Manly (2004)
- MapQTL
- multiple QTL
- van Ooijen, Maliepaard (1996)
- Multimapper
- Bayesian QTL
- Sillanpää, Arjas (1998, 1999)
- MultiQTL
- multiple QTL
- Mester, Ronin, Nevo, Korol (2004)
- PlabQTL
- least squares QTL mapping
- Utz, Melchinger (1994)
- Pseudomarker
- multiple imputation for one or more QTL
- Sen, Churchill (2001)
- QTL Cartographer
- IM, CIM, MIM, MTM
- Basten, Weir, Zeng (1995)
- QTLNetwork
- Yang, Hu, Ye, Zhu (2005)
- R/bqtl
- least squares Bayesian mapping
- Berry CC (1998)
- R/qtl
- QTL diagnostics, IM/EM, multiple imputation
- Sen, Churchill (2001);
Broman, Wu, Sen, Churchill (2003)
- R/qtlbim
- Bayesian interval mapping, epistasis, GxE
- Yi et al. (2005, 2007);
Yandell et al. (2007)
- R/subcon
- meta-analysis for QTL across closely related congenic crosses
- Clee, Yandell et al. (2006)
- WebQTL, GeneNetwork:
- Online QLT mapping using phenotype repositories (gene expression, etc.)
- Wang, Williams, Manly (2003)
- Animal Biotechnology
- Streaming video, UC Davis
- GOLD
- Graphical Overview of Linkage Disequilibrium
- Abecasis, Cookson (2000)
- GDPC
- connecting researchers with multiple integrated data sources
- Casstevens, Buckler (2004)
- GRAMMAR (see also R/GenABEL)
- genome-wide pedigree-based quantitative trait loci association analysis
- Aulchenko, De Koning, Haley (2007)
- GRIDQTL
-
- Seaton et al. (2006)
- Haploview
- analysis and visualization of LD and haplotype maps
- Barrett, Fry, Maller, Daly (2005)
- HAPPY
- fine-mapping quantitative trait loci in outbred animal stocks
- Mott, Talbot, Turri, Collins, Flint (2000)
- JLIN
(java-based linkage disequilibrium plotter)
- Carter, McCaskie, Palmer (2006)
- JoinMap
- linkage maps for multiple crosses
- Stam (1993)
- LDA
- java-based linkage disequilibrium analyzer
- Ding, Zhou, He, Shen (2003)
- Merlin
- rapid analysis of dense genetic maps using sparse gene
flow trees
- Abecasis, Cherny, Cookson, Cardon (2002)
- MIDAS
- analysis and visualisation of interallelic
disequilibrium between multiallelic markers
- Gaunt, Rodriguez, Zapata, Day (2006)
- MTDFREML
- multiple trait derivative free REML
- Boldman et al. (1995); Zhang et al. van Bleck (2006)
- Outmap
- outcrossed trees
- Butcher et al. (2002)
- PowerMarker
- genetic marker analysis
- Liu, Muse (2005)
- QTL Express
- mapping quantitative trait loci in simple and complex pedigrees
- Seaton et al. (2002)
- QxPak
- mixed model statistical framework for inbred lines, within
population studies, or mixtures of populations or crosses;
allows multitrait and multiQTL analyses
- Pérez-Enciso, Misztal (2004)
- R/psmix
- population structure inference via
maximum likelihood
- Wu, Nianjun, Hongyu (2006)
- R/GenABEL
- genome-wide association analysis
- Aulchenko Y (see Aulchenko, De Koning, Haley 2007)
- R/qtl
- four-way cross
- Broman et al. (2003)
- SOLAR
(Sequential Oligogenic Linkage Analysis Routines)
- QTL mapping/variance component analysis in large pedigrees,
possible to include multiple loci, dominance effects, and epistasis.
-
Almasy, Blangero (1998);
Blangero et al. (2000,2001)
- Spagedi
- SPAtial GEnetic structure at the individual or population levels
- Hardy, Vekemans (2002)
- Structure
- inference of population structure using multilocus genotype
data
- Pritchard, Stephens, Donnelly (2000)
- Tassel
- unified mixed-model method for association mapping that
accounts for multiple levels of relatedness
- Yu et al. Buckler (2006);
Zhang, Todhunter, Buckler, van Vleck (2006);
- Unphased
- association and TDT for haplotypes
- Dudbridge (2003)
Return to Statistical Genomics References.
Brian Yandell
(yandell@stat.wisc.edu)