Orthology databases (and ditection methods)

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R
1	Obsolete	Only methodology	Meta-DB or not	Name	Method	Hierarchical/flat/pair-wise (and other characteristics)	Manual curation	Target	#organisms	sequence source	OrthoXML is available	Publication	Last update	version	comment	URL	URL2	paper

2	1			HOVERGEN				vertebrate		Genbank(1994), UniProt(2009)		1994	2009			http://pbil.univ-lyon1.fr/databases/hovergen.php
3				COG	graph, manual	flat, domain-level	yes	prokaryote	1309	NCBI		1997	2020		2003 updated, 2014 extended	http://www.ncbi.nlm.nih.gov/COG/
4				KEGG Orthology	graph, manual	flat	yes	cellular organisms		KEGG GENES		1999	2018		534+5627=6161 ?	http://www.genome.jp/kegg/ko.html
5				HomoloGene		flat		eukaryote	21			2001	2014	build68		http://www.ncbi.nlm.nih.gov/homologene	ftp://ftp.ncbi.nih.gov/pub/HomoloGene/
6				Ensembl Compara	tree	hierarchical		metazoa	227		yes	2002	2019		TreeFam HMM families	https://www.ensembl.org/info/genome/compara/index.html	ftp://ftp.ensembl.org/pub/
7		yes		RIO	tree							2002
8	1			HOPS	tree	domain-based						2003
9				KOG	graph	flat		eukaryote				2003	2003			http://www.ncbi.nlm.nih.gov/COG/
10				MBGD	hybrid	flat (partially hierarchical), domain-level		microbes (and model organisms)	5861	NCBI Assembly Reports	yes	2003	2018			http://mbgd.genome.ad.jp
11				OrthoMCL	graph	flat		eukaryote				2003	2013			http://www.orthomcl.org
12				Panther	tree	hierarchical		eukaryote, prokaryote	104 (65 eukaryotes, 39 prokaryotes)		yes	2003	2018			http://pantherdb.org
13				Evola	hybrid (synteny)							2005	2010			http://www.h-invitational.jp/evola
14			yes (12 methods)	HCOP		pair-wise		human-centric (eukaryotes)	17			2005				http://www.genenames.org/cgi-bin/hcop
15				HOGENOM	tree			microbes				2005	2011			http://pbil.univ-lyon1.fr/databases/hogenom/	ftp://pbil.univ-lyon1.fr/pub/hogenom
16				InParanoid	graph	pair-wise					yes	2005	2013			http://inparanoid.sbc.su.se
17				INVHOGEN (or HOINVGEN)	graph (simple transitive links)	hierarchical		invertebrate		UniProt		2005	2005			http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html
18				OMA	graph	flat or hierarchical or pair-wise			1613		yes	2005	2019			http://omabrowser.org
19				COCO-CL	hybrid (graph-based algorithm for hierarchical group inference)							2006				http://www.rajajothi.com/COCOCL/
20				RoundUp	graph	flat						2006	2013			http://roundup.hms.harvard.edu
21				TreeFam	tree	hierarchical	yes	animal	109			2006	2013			http://www.treefam.org
22			yes	YOGY				eukaryote				2006				http://128.40.79.33/YOGY/
23	1	yes		BLASTO								2007				http://oxytricha.princeton.edu/BlastO/
24		yes		LOFT	graph	hierarchical						2007				https://trac.nbic.nl/loft/
25		yes		Ortholog Clustering on a Multipartite Graph								2007
26				OrthoMam				mammal	116	Ensembl		2007	2019	v10		http://www.orthomam.univ-montp2.fr/orthomam/html/
27				eggNOG	graph	flat		prokaryote, eukaryote	3686			2008	2016			http://eggnog.embl.de
28				GreenPhylDB	hybrid (TribeMCL->PhyML)	hierachical	yes	plant	37			2008	2014			http://www.greenphyl.org
29			yes	OGO								2008				http://miuras.inf.um.es:9080/OGO-1.0/
30				OrthoDB								2008	2018			http://orthodb.org
31				PhylomeDB	tree						yes	2008	2014			http://phylomedb.org
32	1			HOMOLENS				metazoa				2009	2011			http://pbil.univ-lyon1.fr/databases/homolens.php
33				OrthoSelect								2009				http://gobics.de/fabian/orthoselect.php
34				DODO								2010				http://140.109.42.19:16080/dodo_web/home.htm
35	1			FUNGIpath								2010				http://embg.igmors.u-psud.fr/fungipath/
36			yes	MetaPhOrs					826		yes	2010	2014			http://orthology.phylomedb.org
37				OrthoInspector				prokaryote, eukaryote	1688 prokaryotes, 259 eukaryotes			2011	2019		2012 (prokaryotes), 2011 (erkaryotes), 2015 (program)	http://lbgi.fr/orthoinspector/
38				POG				phage				2011	2012			ftp://ftp.ncbi.nlm.nih.gov/pub/kristensen/thousandgenomespogs/
39				OrtholugeDB				prokaryote	2083			2012	2016			http://www.pathogenomics.sfu.ca/ortholugedb/
40				KEGG OC	hybrid (graph-based; quasi-clique)	hierarchical		prokaryote, eukaryote	3903 (3393 bacteria, 207 archaea, 303 eukaryotes)	KEGG GENES		2013	2019			http://www.genome.jp/tools/oc/
41				PGDBj				plant, algae	109 plants, 199 algae			2014	2014			http://pgdbj.jp
42				hOP				human-centric (vertebrates to protozoa)	177			2015	2015			http://web.stanford.edu/group/meyerlab/hOPMAPServer/index.html
43				OrthoFinder								2015	2019
44	1			EGO
45	1			Gene-Oriented Ortholog Database
46	1			MGD
47	1			OrthologID
48	1			P-POD
49	1			PhIGs
50	1			PHOG
51	1			PLAZA				plant				2009	2017	v4.0				https://academic.oup.com/nar/article/46/D1/D1190/4561641/
52	1			ProGMap
53	1			Proteinortho
54				PlantOrDB				plant, algae	41	Phytozome V9		2015
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