International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

C8. Enhancements in Map Manager QTX software for mapping quantitative trait loci

Kenneth F. Manly
Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263-0001

Map Manager QTX software analyzes the results of experimental genetic crosses to map Mendelian and quantitative trait loci (QTLs). It is available in versions for both Microsoft Windows and Mac OS operating systems. Its functions for mapping Mendelian markers include rapid automatic methods for separating newly typed loci into linkage groups and for distributing newly typed loci among previously defined linkage groups. It uses regression to detect and map QTLs by three methods: association with single marker loci, simple interval mapping, and composite interval mapping.

Map Manager QTX was first released in February, 2000 and revisions have been released at monthly intervals since then. Revisions include new functions as well as bug fixes. One important new function is the ability to estimate the genotypes of missing marker data during QTL mapping, using a Markov-chain algorithm described by Jiang and Zeng (Genetica 101: 47-58 (1997)). This improvement makes most data sets more informative and makes Map Manager QTX more equivalent to software which uses maximum-likelihood methods. In addition, Map Manager QTX now supports advanced backcross and advanced intercross designs. Finally, Map Manager QTX now offers weighted regression for recombinant inbred lines in which an estimate of the trait variance is available for each line.

Map Manager QTX will open data files from all previous members of the Map Manager family, and files for the Windows and Mac OS versions can be opened by either version. Map Manager QTX will import and export Mapmaker and Mapmaker/QTL files and it will export data in a formats suitable for QTL Cartographer (

and QGene ( Map Manager QTX and its documentation are available from the Map Manager Web Site (

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Last modified: Saturday, November 3, 2012