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Gene tree correction guided by orthology

Manuel Lafond 1, * Magali Semeria 2 Krister M. Swenson 1, 3 Eric Tannier 2, 4 Nadia El-Mabrouk 1 
* Corresponding author
4 BEAGLE - Artificial Evolution and Computational Biology
LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information, Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Abstract : Background
Reconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, such as conserved synteny.
We explore a way to include external information on orthology in the process of gene tree construction. Given an initial gene tree and a set of orthology constraints on pairs of genes or on clades, we give polynomial-time algorithms for producing a modified gene tree satisfying the set of constraints, that is as close as possible to the original one according to the Robinson-Foulds distance. We assess the validity of the modifications we propose by computing the likelihood ratio between initial and modified trees according to sequence alignments on Ensembl trees, showing that often the two trees are statistically equivalent.
Software and data available upon request to the corresponding author.
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Submitted on : Tuesday, October 15, 2013 - 1:09:16 PM
Last modification on : Monday, May 16, 2022 - 3:00:06 PM



  • HAL Id : hal-00873235, version 1


Manuel Lafond, Magali Semeria, Krister M. Swenson, Eric Tannier, Nadia El-Mabrouk. Gene tree correction guided by orthology. BMC Bioinformatics, BioMed Central, 2013, 14 (Suppl 15), pp.S5. ⟨hal-00873235⟩



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