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
* Auteur correspondant
4 BEAGLE - Artificial Evolution and Computational Biology
LBBE - Laboratoire de Biométrie et Biologie Evolutive, Inria Grenoble - Rhône-Alpes, LIRIS - Laboratoire d'InfoRmatique en Image et Systèmes d'information
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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Soumis le : mardi 15 octobre 2013 - 13:09:16
Dernière modification le : mercredi 16 janvier 2019 - 01:18:00



  • 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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