Table 2. The most commonly used QTL mapping statistical programs for both linkage-based and linkage disequlibrium-based mapping methods, their operating system, and online links.

Name

Version

Platform (operating system)

Description

Availability

References

Online links (verified in July 2009)

Map Manager QTX

b29

Windows, Mac OS

A graphic, interactive program to map quantitative trait loci using intercrosses, backcrosses or recombinant inbred strains in experimental plants or animals.

Free

Manly and Olson, 1999.

http://www.mapmanager.org/mmQTX.html

Mapmaker/QTL

1.1

UNIX, VMS, DOS, Mac OS

A package containing a program for genetic linkage analysis and a program for mapping genes underlying complex traits.

Free

Lincoln et al. 1992.

http://www.broadinstitute.org/ftp/distribution/
software/mapmaker3/

MapQTL

5

Windows ® (95/98/ME/NT4.0/2000/XP/Vista 32-bit

Mapping of quantitative trait loci (QTL) for several types of experimental mapping populations.

Comercial

Van Ooijen, 2009.

http://www.kyazma.nl/index.php/
mc.MapQTL/sc

PlabQTL

1.2

DOS

A program characterizing loci that affect the variation of quantitative traits.

Free

Utz and Melchinger, 2003.

https://www.uni-hohenheim.de/plantbreeding/software/

QGene

4.0

Any computer

An entirely rebuilt Java application that will run on any computer.

Free

Nelson, 1997.

http://www.qgene.org/

QTL Cartographer

2.5 for Windows

UNIX, DOS, Windows, Mac OS

A program to map quantitative traits using a map of molecular markers.

Free

Basten et al. 1994; Wang et al. 2007.

http://statgen.ncsu.edu/qtlcart/index.php

Structure

2.3

DOS, Windows, UNIX (Solaris), Linux

A program for investigating population structure.

Free

Pritchard et al. 2000.

http://pritch.bsd.uchicago.edu/
structure.html

TASSEL

2

Web-based (operating system independent)

A software package for association mapping, diversity estimation and calculating linkage disequilibrium.

Free

Zhang et al. 2006.

http://sourceforge.net/projects/tassel