Gene tree correction guided by orthology

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 t...

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Bibliographic Details
Published in:BMC bioinformatics 2013, Vol.14 Suppl 15 (S15), p.S5-S5, Article S5
Main Authors: Lafond, Manuel, Semeria, Magali, Swenson, Krister M, Tannier, Eric, El-Mabrouk, Nadia
Format: Article
Language:English
Subjects:
Algorithms
Animals
Biochemistry, Molecular Biology
Bioinformatics
Computer Science
Evolution, Molecular
Genes
Genomes
Genomics
Humans
Leaves
Life Sciences
Molecular biology
Phylogeny
Proceedings
Quantitative Methods
Sequence Alignment
Software
Synteny
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Summary: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.
ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-14-S15-S5