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Duplication and Inversion History of a Tandemly Repeated Genes Family

Mathieu Lajoie 1, 2 Denis Bertrand 1 Nadia El-Mabrouk 1 Olivier Gascuel 2, * 
* Corresponding author
2 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
Abstract : Given a phylogenetic tree for a family of tandemly repeated genes and their signed order on the chromosome, we aim to find the minimum number of inversions compatible with an evolutionary history of this family. This is the first attempt to account for inversions in an evolutionary model of tandemly repeated genes. We present a branch-and-bound algorithm that finds the exact solution, and a polynomial-time heuristic based on the breakpoint distance. We show, on simulated data, that those algorithms can be used to improve phylogenetic inference of tandemly repeated gene families. An application on a published phylogeny of KRAB zinc finger genes is presented.
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Submitted on : Thursday, November 29, 2007 - 7:29:00 PM
Last modification on : Friday, August 5, 2022 - 3:02:17 PM
Long-term archiving on: : Monday, April 12, 2010 - 5:34:55 AM


  • HAL Id : lirmm-00192954, version 1



Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk, Olivier Gascuel. Duplication and Inversion History of a Tandemly Repeated Genes Family. Journal of Computational Biology, Mary Ann Liebert, 2007, 14 (4), pp.462-478. ⟨lirmm-00192954⟩



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