Bioinformatics Vol. 18 no. 2 2002
Pages 339-340
© 2002 Oxford University Press
Applications Note |
QTL Express: mapping quantitative trait loci in simple and complex pedigrees
1 Institute of Cell, Animal and Population
Biology, University of Edinburgh, West Mains Road, Edinburgh EH9
3JT, UK
2 Roslin Institute (Edinburgh), Roslin,
Midlothian EH25 9PS, UK
3 School of Biosciences, University of
Birmingham, Edgbaston, Birmingham B15 2TT, UK
Received on June 27, 2001
; revised on August 24, 2001
; accepted on September 5, 2001
Summary: QTL Express is the first application for Quantitative Trait Locus (QTL) mapping in outbred populations with a web-based user interface. User input of three files containing a marker map, trait data and marker genotypes allows mapping of single or multiple QTL by the regression approach, with the option to perform permutation or bootstrap tests.
Availability: http://qtl.cap.ed.ac.uk/
Contact: george.seaton{at}ed.ac.uk
* To whom correspondence should be addressed.
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|
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|
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
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|
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|
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