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IRILmap : Linkage map distance conversion software for Intermated Recombinant Inbred Lines

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Project leader Matthieu Falque (contact)



Intermated recombinant inbred lines (IRILs) are obtained by including generations of intermating among F2 individuals before selfing or sib-mating. Compared to usual recombinant inbred lines (RILs), such IRILs offer an increase of map resolution, due to additional recombination events occurring during intermating generations (Liu et al., 1996, Genetics 142:247-258).
Based on the reference work of Haldane and Waddington (1931, Genetics 16: 357-374) on RILs, theoretical developments were carried out more recently by Winkler et al. (2003, Genetics 164: 741-745) to establish the relationship between the recombination Rn observed in an IRIL population obtained with n generations of random intermating, and the recombination fraction r per meiosis.
IRILmap was developed to compute "actual" centiMorgan distances from MapMaker output files (result of "Map" command obtained with the "photo" command) obtained from IRIL data with "RI self" or "RI sib" options (see "Distance calculation" section for details). It is also possible to use IRILmap to convert Haldane distances into Kosambi's, or reciprocally. Mapping data produced with other software than MapMaker can be used, provided that file formats are respected (see "Format specifications" section for details) and that distances were computed as for RILs by using Haldane & Waddington's formula. For this purpose, tabulated files are also accepted in addition to MapMaker output files.

“IRILmap.exe” was compiled to run on Windows-based platforms.

The perl script “RIL2IRIL” is also included in the package, to perform similar distance conversions from UNIX or LINUX shell. This script reads no file, but accepts one input distance value as argument and returns the converted distance. It is then easy to embed in any shell, perl, or other type application.

Upon request, we may consider producing executables for other platforms.

Reference
Falque M. IRILmap: linkage map distance correction for intermated recombinant inbred
lines/advanced recombinant inbred strains. Bioinformatics. (2005) Aug 15;21(16):3441-2

Download
IRILmap is available for free IRILmap_v1_1

Acknowledgements
Thanks to Christine Dillmann, Frédéric Hospital, Olivier Martin, Laurence Moreau, and Dominique de Vienne for helpful discussion on IRIL calculations, and to Marie-Cécile Leclerc-Falque and Johann Joets for assistance in software development.

Legal notice
Program: IRILmap Version: 1.1
Copyright © 2004 by Matthieu Falque.
All rights reserved.
This package should not be redistributed or used for any commercial purpose, without written permission from the authors.This package is provided``AS IS'' and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose, are disclaimed. In no event shall the authors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but notlimited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.