Distinguishing homologous from analogous proteins. Systematic zoology, pp.99-113, 1970. ,
Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs, PLoS Computational Biology, vol.7, issue.5, p.1002514 ,
DOI : 10.1371/journal.pcbi.1002514.s022
Gene Family Level Comparative Analysis of Gene Expression in Mammals Validates the Ortholog Conjecture, Genome Biology and Evolution, vol.6, issue.4, pp.754-762 ,
DOI : 10.1093/gbe/evu051
Functional and evolutionary implications of gene orthology, Nature Reviews Genetics, vol.8, issue.5, pp.360-366 ,
DOI : 10.1093/nar/25.17.3389
Orthology, paralogy and proposed classification for paralog subtypes, Trends in Genetics, vol.18, issue.12, pp.619-620, 2002. ,
DOI : 10.1016/S0168-9525(02)02793-2
The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study, PloS one, vol.8, issue.2, p.56925, 2013. ,
Phylogenetic and Functional Assessment of Orthologs Inference
Projects and Methods, PLoS Computational Biology, vol.19, issue.1, p.1000262, 2009. ,
DOI : 10.1371/journal.pcbi.1000262.s018
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, PLoS ONE, vol.17, issue.4, p.383, 2007. ,
DOI : 10.1371/journal.pone.0000383.s008
Evaluating Ortholog Prediction Algorithms in a Yeast Model
Clade, PLoS ONE, vol.449, issue.4, p.18755, 2011. ,
DOI : 10.1371/journal.pone.0018755.s002
Positional orthology: putting genomic evolutionary relationships into context, Briefings in Bioinformatics, vol.12, issue.5, pp.401-413 ,
DOI : 10.1093/bib/bbr040
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178058
Exploitation of gene context. Current opinion in structural biology, pp.366-70, 2000. ,
The evolutionary dynamics of eukaryotic gene order, Nature Reviews Genetics, vol.5, issue.4, pp.299-310, 2004. ,
DOI : 10.1038/nature01107
Genome Alignment, Evolution of Prokaryotic Genome Organization, and Prediction of Gene Function Using Genomic Context, Genome Research, vol.11, issue.3, pp.356-72, 2001. ,
DOI : 10.1101/gr.GR-1619R
Computational methods for Gene Orthology inference, Briefings in Bioinformatics, vol.12, issue.5, pp.379-91, 2011. ,
DOI : 10.1093/bib/bbr030
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178053
Automated ortholog inference from phylogenetic trees and calculation of orthology reliability, Bioinformatics, vol.18, issue.1, pp.92-101, 2002. ,
DOI : 10.1093/bioinformatics/18.1.92
Rio: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs, BMC bioinformatics, vol.19, pp.1-19, 2002. ,
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score, Nucleic Acids Research, vol.39, issue.5, p.32, 2011. ,
DOI : 10.1093/nar/gkq953
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions, Nucleic Acids Research, vol.39, issue.Database, pp.39556-60, 2011. ,
DOI : 10.1093/nar/gkq1109
From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem, Molecular Phylogenetics and Evolution, vol.7, issue.2, pp.231-240, 1997. ,
DOI : 10.1006/mpev.1996.0390
Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes, PLoS Genetics, vol.13, issue.1, 2011. ,
DOI : 10.1371/journal.pgen.1001284.s007
URL : https://hal.archives-ouvertes.fr/pasteur-00578535
Analysis of long branch extraction and long branch shortening, BMC genomics, vol.11, issue.2, p.14, 2010. ,
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.3, pp.403-410, 1990. ,
DOI : 10.1016/S0022-2836(05)80360-2
Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981. ,
DOI : 10.1016/0022-2836(81)90087-5
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes, Genome Research, vol.13, issue.9, pp.2178-89, 2003. ,
DOI : 10.1101/gr.1224503
Inparanoid: a comprehensive database of eukaryotic orthologs, Nucleic Acids Research, vol.33, issue.Database issue, pp.476-480, 2005. ,
DOI : 10.1093/nar/gki107
OMA 2011: orthology inference among 1000 complete genomes, Nucleic Acids Research, vol.39, issue.Database, pp.39289-94, 2011. ,
DOI : 10.1093/nar/gkq1238
URL : http://doi.org/10.1093/nar/gkq1238
Roundup: a multi-genome repository of orthologs and evolutionary distances, Bioinformatics, vol.22, issue.16, pp.222044-2046, 2006. ,
DOI : 10.1093/bioinformatics/btl286
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world, Nucleic Acids Research, vol.36, issue.21, pp.6688-6719, 2008. ,
DOI : 10.1093/nar/gkn668
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages, Proceedings of the National Academy of Sciences, vol.106, issue.18, pp.1067273-7280, 2009. ,
DOI : 10.1073/pnas.0901808106
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
DOI : 10.1093/nar/gkh340
HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.39, issue.suppl, pp.29-37, 2011. ,
DOI : 10.1093/nar/gkr367
URL : http://doi.org/10.1093/nar/gkr367
The use of gene clusters to infer functional coupling, Proceedings of the National Academy of Sciences, vol.96, issue.6, pp.2896-901, 1999. ,
DOI : 10.1073/pnas.96.6.2896
Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data, BMC Evolutionary Biology, vol.7, issue.1, p.237, 2007. ,
DOI : 10.1186/1471-2148-7-237
URL : https://hal.archives-ouvertes.fr/hal-00194466
Mcl a cluster algorithm for graphs, the Netherlands, pp.1-40, 2000. ,
Phylip (phylogeny inference package) version 3.6, 2005. ,
Orthology prediction methods: a quality assessment using curated protein families. BioEssays: news and reviews in molecular, pp.33769-80, 2011. ,
Joining forces in the quest for orthologs, Genome Biology, vol.10, issue.9, p.403, 2009. ,
DOI : 10.1186/gb-2009-10-9-403
Toward community standards in the quest for orthologs, Bioinformatics, vol.28, issue.6, pp.900-904 ,
DOI : 10.1093/bioinformatics/bts050
A new measure for functional similarity of gene products based on gene ontology, BMC Bioinformatics, vol.7, issue.1, p.302, 2006. ,
DOI : 10.1186/1471-2105-7-302
History of the enzyme nomenclature system, Bioinformatics, vol.16, issue.1, pp.34-40, 2000. ,
DOI : 10.1093/bioinformatics/16.1.34
Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000. ,
DOI : 10.1038/75556
OrthoInspector: comprehensive orthology analysis and visual exploration, BMC Bioinformatics, vol.12, issue.1, p.11, 2011. ,
DOI : 10.1186/1471-2105-12-11
URL : https://hal.archives-ouvertes.fr/inserm-00663697
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees, Nucleic Acids Research, vol.41, issue.D1, pp.41377-86 ,
DOI : 10.1093/nar/gks1118