GENOPLANTE © MCQTL | ||
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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.
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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 |
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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!
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Register |
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Registred users can click here |
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New bug reporting system |
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Members of MCQTL team and contacts:
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