Gene tree correction guided by orthology

[摘要] BackgroundReconciled 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.ResultsWe 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.AvailabilitySoftware and data available upon request to the corresponding author.

[发布日期] 2013-10-15

[关键词] Gene Tree;Corrected Tree;Extant Gene;Binary Resolution;Lower Common Ancestor