The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements, Nucleic Acids Res, vol.43, pp.240-249, 2014. ,
Standardized benchmarking in the quest for orthologs, Nat. Methods, vol.13, pp.425-430, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01636892
Quest for orthologs entails quest for tree of life: in search of the gene stream, Genome Biol. Evol, vol.7, pp.1988-1999, 2015. ,
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction, Nucleic Acids Res, vol.43, pp.136-143, 2011. ,
URL : https://hal.archives-ouvertes.fr/lirmm-01283940
The Orthology Ontology: development and applications, J. Biomed. Semant, vol.7, p.34, 2016. ,
Functional and evolutionary implications of gene orthology, Nat. Rev. Genet, vol.14, pp.360-366, 2013. ,
Phylogenetic-based propagation of functional annotations within the, Gene Ontology consortium. Brief. Bioinf, vol.12, pp.449-462, 2011. ,
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology, BMC Genomics, p.81, 2010. ,
Irrational exuberance for resolved species trees, Evolution, vol.70, pp.7-17, 2015. ,
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets, Bioinformatics, vol.32, pp.1323-1330, 2016. ,
Synthesis of phylogeny and taxonomy into a comprehensive tree of life, Proc. Natl. Acad. Sci. USA, vol.112, pp.12764-12769, 2015. ,
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Res, vol.44, pp.286-293, 2016. ,
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software, Nucleic Acids Res, vol.43, pp.250-256, 2014. ,
What makes a sodium channel?, J. Gen. Physiol, vol.148, pp.89-90, 2016. ,
Applications of comparative evolution to human disease genetics, Curr. Opin. Genet. Dev, vol.35, pp.16-24, 2015. ,
PANTHER version 10: expanded protein families and functions, and analysis tools, Nucleic Acids Res, vol.44, pp.336-342, 2015. ,
Comparative co-expression analysis in plant biology, Plant Cell Environ, vol.35, pp.1787-1798, 2012. ,
Testing the ortholog conjecture with comparative functional genomic data from mammals, PLoS Comput. Biol, vol.7, p.1002073, 2011. ,
A meta-approach for improving the prediction and the functional annotation of ortholog groups, BMC Genomics, vol.15, p.16, 2014. ,
URL : https://hal.archives-ouvertes.fr/inserm-01229454
PLAZA 3.0: an access point for plant comparative genomics, Nucleic Acids Res, vol.43, pp.974-981, 2014. ,
Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information, Brief. Bioinf, vol.12, pp.485-488, 2011. ,
Hieranoid: hierarchical orthology inference, J. Mol. Biol, vol.425, pp.2072-2081, 2013. ,
TreeFam v9: a new website, more species and orthology-on-the-fly, Nucleic Acids Res, vol.42, pp.922-925, 2014. ,
Big data and other challenges in the quest for orthologs, Bioinformatics, vol.30, pp.2993-2998, 2014. ,
Orthology, paralogy and proposed classification for paralog subtypes, Trends in Genet, vol.18, pp.619-620, 2002. ,
CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool, Front. Plant Sci, vol.6, p.1194, 2016. ,
The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks, Nucleic Acids Res, vol.42, pp.643-648, 2013. ,