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OMA 2011: orthology inference among 1000 complete genomes.

Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C.

Nucleic Acids Res. 2011 Jan;39(Database issue):D289-94. doi: 10.1093/nar/gkq1238. Epub 2010 Nov 27.


The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.

Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D240-9. doi: 10.1093/nar/gku1158. Epub 2014 Nov 15.


Algorithm of OMA for large-scale orthology inference.

Roth AC, Gonnet GH, Dessimoz C.

BMC Bioinformatics. 2008 Dec 4;9:518. doi: 10.1186/1471-2105-9-518. Erratum in: BMC Bioinformatics.2009;10. doi:10.1186/1471-2105-10-220.


The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D, de Farias TM, Zile K, Stevenson C, Long J, Redestig H, Gonnet GH, Dessimoz C.

Nucleic Acids Res. 2018 Jan 4;46(D1):D477-D485. doi: 10.1093/nar/gkx1019.


OMA Browser--exploring orthologous relations across 352 complete genomes.

Schneider A, Dessimoz C, Gonnet GH.

Bioinformatics. 2007 Aug 15;23(16):2180-2. Epub 2007 Jun 1.


Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference.

Train CM, Glover NM, Gonnet GH, Altenhoff AM, Dessimoz C.

Bioinformatics. 2017 Jul 15;33(14):i75-i82. doi: 10.1093/bioinformatics/btx229.


Inferring hierarchical orthologous groups from orthologous gene pairs.

Altenhoff AM, Gil M, Gonnet GH, Dessimoz C.

PLoS One. 2013;8(1):e53786. doi: 10.1371/journal.pone.0053786. Epub 2013 Jan 14.


The Microbe browser for comparative genomics.

Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W296-9. doi: 10.1093/nar/gkp268. Epub 2009 Apr 30.


BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

Di L, Pagan PE, Packer D, Martin CL, Akther S, Ramrattan G, Mongodin EF, Fraser CM, Schutzer SE, Luft BJ, Casjens SR, Qiu WG.

BMC Bioinformatics. 2014 Jul 3;15:233. doi: 10.1186/1471-2105-15-233.


OrthologID: automation of genome-scale ortholog identification within a parsimony framework.

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R.

Bioinformatics. 2006 Mar 15;22(6):699-707. Epub 2006 Jan 12.


BGD: a database of bat genomes.

Fang J, Wang X, Mu S, Zhang S, Dong D.

PLoS One. 2015 Jun 25;10(6):e0131296. doi: 10.1371/journal.pone.0131296. eCollection 2015.


QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence.

Yu C, Desai V, Cheng L, Reifman J.

BMC Bioinformatics. 2012 Jun 22;13:143. doi: 10.1186/1471-2105-13-143.


OrthoDB: the hierarchical catalog of eukaryotic orthologs.

Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D271-5. Epub 2007 Oct 18.


A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation.

Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P.

PLoS One. 2014 Nov 4;9(11):e111122. doi: 10.1371/journal.pone.0111122. eCollection 2014.


Gene-oriented ortholog database: a functional comparison platform for orthologous loci.

Ho MR, Chen CH, Lin WC.

Database (Oxford). 2010;2010:baq002. doi: 10.1093/database/baq002. Epub 2010 Feb 10.


ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.

Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I.

Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54. doi: 10.1093/nar/gkn684. Epub 2008 Oct 9.


Orthology prediction methods: a quality assessment using curated protein families.

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P.

Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011 Aug 19.


TreeFam v9: a new website, more species and orthology-on-the-fly.

Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A.

Nucleic Acids Res. 2014 Jan;42(Database issue):D922-5. doi: 10.1093/nar/gkt1055. Epub 2013 Nov 4.


OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simão FA, Pozdnyakov IA, Ioannidis P, Zdobnov EM.

Nucleic Acids Res. 2015 Jan;43(Database issue):D250-6. doi: 10.1093/nar/gku1220. Epub 2014 Nov 26.


OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.

Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV.

Nucleic Acids Res. 2013 Jan;41(Database issue):D358-65. doi: 10.1093/nar/gks1116. Epub 2012 Nov 24.

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