The aim of MCQTL software package is to perform QTL mapping in multi-cross design. It allows to study the usual populations derived from inbred lines and proposes to link the families by assuming that the QTL locations are the same in all them. Moreover, a connected modelling of the QTL genotypic effect is allowed in multiple related families.
The implemented model is a linear regression model in which the probabilities of QTL genotypes given marker information are used as regressors (Haley and Knott, 1992). A composite interval mapping (Zeng, 1993) and an iterative QTL mapping are implemented (Charcosset et al., 2000) to deal with multiple QTL model. Marker cofactor selections by forward or backward stepwise methods are implemented as well as computation of threshold test value by permutation (Churchill and Doerge, 1994).
Finally, the model parameters are estimated. More precisely, Pvalues of the Fisher test at the QTL locations, LOD support intervals, QTL effect and residual parameter estimates, model and QTL percentage of explained variance are provided.
MCQTL package is composed of three software applications. The first component reads the data from MAPMAKER files. The second component, ProbaPop, computes QTL genotype probabilities at specific chromosome location given multiple marker data in each family and stores them in XML formatted files. The last component, Multipop, builds the joint model and fits the observations on genotype probabilities.
MCQTL runs on Linux platforms.
MCQTL can use Linkage Disequilibrium (LD) information. You may download free R package clusthaplo here in order to produce LD files for Multipop.

Reference User Manual Plant Animal Genome 2006 - Poster
Bioinformatics 2005, 21, 128-130 User Manual (pdf file) Outbred supplement (pdf file) POSTER_PAG_2006.pdf

To download MCQTL software application, yo have to register first. Then after Administrator validation, you will receive a user/password and a link to the download page. Please register now!

Registred users can click here

New bug reporting system

Members of MCQTL team and contacts:
  • Brigitte Mangin
  • Sylvain Jasson
  • Bertrand Escaliere
  • Stéphane Lambert
  • David Delannoy
  • Marie-Francoise Jourjon
  • Remi Cathelin
  • Baba Ngom
  • Jacques Marcel