Large-scale assignment of orthology: back to phylogenetics?
Open Access
- 1 January 2008
- journal article
- review article
- Published by Springer Nature in Genome Biology
- Vol. 9 (10) , 235
- https://doi.org/10.1186/gb-2008-9-10-235
Abstract
Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies.Keywords
This publication has 35 references indexed in Scilit:
- Automatic genome-wide reconstruction of phylogenetic gene treesBioinformatics, 2007
- Benchmarking ortholog identification methods using functional genomics dataGenome Biology, 2006
- OrthologID: automation of genome-scale ortholog identification within a parsimony frameworkBioinformatics, 2006
- Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotesBioinformatics, 2005
- Evolution of Proteins and Proteomes: A Phylogenetics ApproachEvolutionary Bioinformatics, 2005
- Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)Genome Research, 2002
- A simple algorithm to infer gene duplication and speciation events on a gene treeBioinformatics, 2001
- Gene Family Evolution and Homology: Genomics Meets PhylogeneticsAnnual Review of Genomics and Human Genetics, 2000
- Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary AnalysisGenome Research, 1998
- Distinguishing Homologous from Analogous ProteinsSystematic Zoology, 1970