Sequence homology (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Sequence homology" in English language version.

refsWebsite

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91nih.gov

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56doi.org

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15harvard.edu

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4semanticscholar.org

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3zenodo.org

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2treefam.org

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1ebi.ac.uk

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1scu.edu

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1worldcat.org

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1jstor.org

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1embl.de

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1greenphyl.org

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1su.se

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1curie.fr

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1nyu.edu

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1univ-montp2.fr

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1orthomcl.org

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1davidemms.github.io

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1unil.ch

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1phylogenomics.blogspot.com

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curie.fr

ohnologs.curie.fr

"Vertebrate Ohnologs". ohnologs.curie.fr. Retrieved 2018-10-12.

davidemms.github.io

OrthoFinder: Orthologs from gene trees
Emms DM, Kelly S (November 2019). "OrthoFinder: phylogenetic orthology inference for comparative genomics". Genome Biology. 20 (1): 238. doi:10.1186/s13059-019-1832-y. PMC 6857279. PMID 31727128.

doi.org

Koonin EV (2005). "Orthologs, paralogs, and evolutionary genomics". Annual Review of Genetics. 39: 309–38. doi:10.1146/annurev.genet.39.073003.114725. PMID 16285863.
Reeck GR, de Haën C, Teller DC, Doolittle RF, Fitch WM, Dickerson RE, et al. (August 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Cell. 50 (5): 667. doi:10.1016/0092-8674(87)90322-9. PMID 3621342. S2CID 42949514.
Fitch WM (June 1970). "Distinguishing homologous from analogous proteins". Systematic Zoology. 19 (2): 99–113. doi:10.2307/2412448. JSTOR 2412448. PMID 5449325. Where the homology is the result of gene duplication so that both copies have descended side by side during the history of an organism (for example, a and b hemoglobin) the genes should be called paralogous (para = in parallel). Where the homology is the result of speciation so that the history of the gene reflects the history of the species (for example a hemoglobin in man and mouse) the genes should be called orthologous (ortho = exact).
Falciatore A, Merendino L, Barneche F, Ceol M, Meskauskiene R, Apel K, Rochaix JD (January 2005). "The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas". Genes & Development. 19 (1): 176–87. doi:10.1101/gad.321305. PMC 540235. PMID 15630026.
Fang G, Bhardwaj N, Robilotto R, Gerstein MB (March 2010). "Getting started in gene orthology and functional analysis". PLOS Computational Biology. 6 (3): e1000703. Bibcode:2010PLSCB...6E0703F. doi:10.1371/journal.pcbi.1000703. PMC 2845645. PMID 20361041.
COGs: Clusters of Orthologous Groups of proteins
Tatusov RL, Koonin EV, Lipman DJ (October 1997). "A genomic perspective on protein families". Science. 278 (5338): 631–7. Bibcode:1997Sci...278..631T. doi:10.1126/science.278.5338.631. PMID 9381173.
Correia K, Yu SM, Mahadevan R (January 2019). "AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution". Database. 2019. doi:10.1093/database/baz022. PMC 6425859. PMID 30893420.
eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. (January 2010). "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations". Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. (January 2014). "eggNOG v4.0: nested orthology inference across 3686 organisms". Nucleic Acids Research. 42 (Database issue): D231-9. doi:10.1093/nar/gkt1253. PMC 3964997. PMID 24297252.
GreenPhylDB
Conte MG, Gaillard S, Lanau N, Rouard M, Périn C (January 2008). "GreenPhylDB: a database for plant comparative genomics". Nucleic Acids Research. 36 (Database issue): D991-8. doi:10.1093/nar/gkm934. PMC 2238940. PMID 17986457.
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, et al. (January 2011). "GreenPhylDB v2.0: comparative and functional genomics in plants". Nucleic Acids Research. 39 (Database issue): D1095-102. doi:10.1093/nar/gkq811. PMC 3013755. PMID 20864446.
Inparanoid: Eukaryotic Ortholog Groups
Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, et al. (January 2010). "InParanoid 7: new algorithms and tools for eukaryotic orthology analysis". Nucleic Acids Research. 38 (Database issue): D196-203. doi:10.1093/nar/gkp931. PMC 2808972. PMID 19892828.
Sonnhammer EL, Östlund G (January 2015). "InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic". Nucleic Acids Research. 43 (Database issue): D234-9. doi:10.1093/nar/gku1203. PMC 4383983. PMID 25429972.
Singh PP, Arora J, Isambert H (July 2015). "Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes". PLOS Computational Biology. 11 (7): e1004394. Bibcode:2015PLSCB..11E4394S. doi:10.1371/journal.pcbi.1004394. PMC 4504502. PMID 26181593.
Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D, et al. (January 2018). "The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces". Nucleic Acids Research. 46 (D1): D477 – D485. doi:10.1093/nar/gkx1019. PMC 5753216. PMID 29106550.
Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, et al. (January 2017). "OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs". Nucleic Acids Research. 45 (D1): D744 – D749. doi:10.1093/nar/gkw1119. PMC 5210582. PMID 27899580.
Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, et al. (January 2019). "OrthoInspector 3.0: open portal for comparative genomics". Nucleic Acids Research. 47 (D1): D411 – D418. doi:10.1093/nar/gky1068. PMC 6323921. PMID 30380106.
OrthologID
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R (March 2006). "OrthologID: automation of genome-scale ortholog identification within a parsimony framework". Bioinformatics. 22 (6): 699–707. doi:10.1093/bioinformatics/btk040. PMID 16410324.
Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R (2009). "Gene orthology assessment with OrthologID". In Posada D (ed.). Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology. Vol. 537. Humana Press. pp. 23–38. doi:10.1007/978-1-59745-251-9_2. ISBN 978-1-59745-251-9. PMID 19378138.
OrthoMaM
Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJ (November 2007). "OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics". BMC Evolutionary Biology. 7 (1): 241. Bibcode:2007BMCEE...7..241R. doi:10.1186/1471-2148-7-241. PMC 2249597. PMID 18053139.
Douzery EJ, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V (July 2014). "OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals". Molecular Biology and Evolution. 31 (7): 1923–8. doi:10.1093/molbev/msu132. PMID 24723423.
Scornavacca C, Belkhir K, Lopez J, Dernat R, Delsuc F, Douzery EJ, Ranwez V (April 2019). "OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes". Molecular Biology and Evolution. 36 (4): 861–862. doi:10.1093/molbev/msz015. PMC 6445298. PMID 30698751.
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Chen F, Mackey AJ, Stoeckert CJ, Roos DS (January 2006). "OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups". Nucleic Acids Research. 34 (Database issue): D363-8. doi:10.1093/nar/gkj123. PMC 1347485. PMID 16381887.
Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, et al. (September 2011). "Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups". Current Protocols in Bioinformatics. Chapter 6 (1): Unit 6.12.1–19. doi:10.1002/0471250953.bi0612s35. ISBN 978-0471250951. PMC 3196566. PMID 21901743.
Roundup
Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP (August 2006). "Roundup: a multi-genome repository of orthologs and evolutionary distances". Bioinformatics. 22 (16): 2044–6. doi:10.1093/bioinformatics/btl286. PMID 16777906.
Cosentino, Salvatore; Iwasaki, Wataru (1 January 2019). "SonicParanoid: fast, accurate and easy orthology inference". Bioinformatics. 35 (1): 149–151. doi:10.1093/bioinformatics/bty631. PMC 6298048. PMID 30032301.
Cosentino, Salvatore; Sriswasdi, Sira; Iwasaki, Wataru (25 July 2024). "SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models". Genome Biology. 25 (1). doi:10.1186/s13059-024-03298-4. PMC 11270883.
TreeFam: Tree families database
van der Heijden RT, Snel B, van Noort V, Huynen MA (March 2007). "Orthology prediction at scalable resolution by phylogenetic tree analysis". BMC Bioinformatics. 8: 83. doi:10.1186/1471-2105-8-83. PMC 1838432. PMID 17346331.
TreeFam: Tree families database
Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, et al. (January 2008). "TreeFam: 2008 Update". Nucleic Acids Research. 36 (Database issue): D735-40. doi:10.1093/nar/gkm1005. PMC 2238856. PMID 18056084.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A (January 2014). "TreeFam v9: a new website, more species and orthology-on-the-fly". Nucleic Acids Research. 42 (Database issue): D922-5. doi:10.1093/nar/gkt1055. PMC 3965059. PMID 24194607.
OrthoFinder: Orthologs from gene trees
Emms DM, Kelly S (November 2019). "OrthoFinder: phylogenetic orthology inference for comparative genomics". Genome Biology. 20 (1): 238. doi:10.1186/s13059-019-1832-y. PMC 6857279. PMID 31727128.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (February 2009). "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates". Genome Research. 19 (2): 327–35. doi:10.1101/gr.073585.107. PMC 2652215. PMID 19029536.
Thanki AS, Soranzo N, Haerty W, Davey RP (March 2018). "GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline". GigaScience. 7 (3): 1–10. doi:10.1093/gigascience/giy005. PMC 5863215. PMID 29425291.
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, et al. (January 2011). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 39 (Database issue): D38-51. doi:10.1093/nar/gkq1172. PMC 3013733. PMID 21097890.
Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS (May 2006). "Improving the specificity of high-throughput ortholog prediction". BMC Bioinformatics. 7: 270. doi:10.1186/1471-2105-7-270. PMC 1524997. PMID 16729895.
Zakany J, Duboule D (August 2007). "The role of Hox genes during vertebrate limb development". Current Opinion in Genetics & Development. 17 (4): 359–66. doi:10.1016/j.gde.2007.05.011. PMID 17644373.
Studer RA, Robinson-Rechavi M (May 2009). "How confident can we be that orthologs are similar, but paralogs differ?". Trends in Genetics. 25 (5): 210–6. doi:10.1016/j.tig.2009.03.004. PMID 19368988.
Nehrt NL, Clark WT, Radivojac P, Hahn MW (June 2011). "Testing the ortholog conjecture with comparative functional genomic data from mammals". PLOS Computational Biology. 7 (6): e1002073. Bibcode:2011PLSCB...7E2073N. doi:10.1371/journal.pcbi.1002073. PMC 3111532. PMID 21695233.
Noda-Garcia L, Romero Romero ML, Longo LM, Kolodkin-Gal I, Tawfik DS (July 2017). "Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation". EMBO Reports. 18 (7): 1139–1149. doi:10.15252/embr.201743990. PMC 5494520. PMID 28468957.
Lundin LG (April 1993). "Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse". Genomics. 16 (1): 1–19. doi:10.1006/geno.1993.1133. PMID 8486346.
Coulier F, Popovici C, Villet R, Birnbaum D (December 2000). "MetaHox gene clusters". The Journal of Experimental Zoology. 288 (4): 345–51. Bibcode:2000JEZ...288..345C. doi:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y. PMID 11144283.
Ruddle FH, Bentley KL, Murtha MT, Risch N (1994). "Gene loss and gain in the evolution of the vertebrates". Development. 1994: 155–61. doi:10.1242/dev.1994.Supplement.155. PMID 7579516.
Pébusque MJ, Coulier F, Birnbaum D, Pontarotti P (September 1998). "Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution". Molecular Biology and Evolution. 15 (9): 1145–59. doi:10.1093/oxfordjournals.molbev.a026022. PMID 9729879.
Larsson TA, Olsson F, Sundstrom G, Lundin LG, Brenner S, Venkatesh B, Larhammar D (June 2008). "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions". BMC Evolutionary Biology. 8 (1): 184. Bibcode:2008BMCEE...8..184L. doi:10.1186/1471-2148-8-184. PMC 2453138. PMID 18578868.
Pollard SL, Holland PW (September 2000). "Evidence for 14 homeobox gene clusters in human genome ancestry". Current Biology. 10 (17): 1059–62. Bibcode:2000CBio...10.1059P. doi:10.1016/S0960-9822(00)00676-X. PMID 10996074. S2CID 32135432.
Mulley JF, Chiu CH, Holland PW (July 2006). "Breakup of a homeobox cluster after genome duplication in teleosts". Proceedings of the National Academy of Sciences of the United States of America. 103 (27): 10369–10372. Bibcode:2006PNAS..10310369M. doi:10.1073/pnas.0600341103. PMC 1502464. PMID 16801555.
Flajnik MF, Kasahara M (September 2001). "Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system". Immunity. 15 (3): 351–62. doi:10.1016/S1074-7613(01)00198-4. PMID 11567626.
McLysaght A, Hokamp K, Wolfe KH (June 2002). "Extensive genomic duplication during early chordate evolution". Nature Genetics. 31 (2): 200–4. doi:10.1038/ng884. PMID 12032567. S2CID 8263376.
Wolfe K (May 2000). "Robustness--it's not where you think it is". Nature Genetics. 25 (1): 3–4. doi:10.1038/75560. PMID 10802639. S2CID 85257685.
Singh PP, Affeldt S, Cascone I, Selimoglu R, Camonis J, Isambert H (November 2012). "On the expansion of "dangerous" gene repertoires by whole-genome duplications in early vertebrates". Cell Reports. 2 (5): 1387–98. doi:10.1016/j.celrep.2012.09.034. PMID 23168259.
Malaguti G, Singh PP, Isambert H (May 2014). "On the retention of gene duplicates prone to dominant deleterious mutations". Theoretical Population Biology. 93: 38–51. Bibcode:2014TPBio..93...38M. doi:10.1016/j.tpb.2014.01.004. PMID 24530892.
Singh PP, Affeldt S, Malaguti G, Isambert H (July 2014). "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". PLOS Computational Biology. 10 (7): e1003754. Bibcode:2014PLSCB..10E3754S. doi:10.1371/journal.pcbi.1003754. PMC 4117431. PMID 25080083.
McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA (January 2014). "Ohnologs are overrepresented in pathogenic copy number mutations". Proceedings of the National Academy of Sciences of the United States of America. 111 (1): 361–6. Bibcode:2014PNAS..111..361M. doi:10.1073/pnas.1309324111. PMC 3890797. PMID 24368850.
Makino T, McLysaght A (May 2010). "Ohnologs in the human genome are dosage balanced and frequently associated with disease". Proceedings of the National Academy of Sciences of the United States of America. 107 (20): 9270–4. Bibcode:2010PNAS..107.9270M. doi:10.1073/pnas.0914697107. PMC 2889102. PMID 20439718.
Glover NM, Redestig H, Dessimoz C (July 2016). "Homoeologs: What Are They and How Do We Infer Them?". Trends in Plant Science. 21 (7). Cell Press: 609–621. Bibcode:2016TPS....21..609G. doi:10.1016/j.tplants.2016.02.005. PMC 4920642. PMID 27021699.
García-Moreno J, Mindell DP (December 2000). "Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD". Molecular Biology and Evolution. 17 (12): 1826–32. doi:10.1093/oxfordjournals.molbev.a026283. PMID 11110898.

ebi.ac.uk

"Clustal FAQ #Symbols". Clustal. Retrieved 8 December 2014.

embl.de

eggnog.embl.de

eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. (January 2010). "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations". Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.

greenphyl.org

GreenPhylDB
Conte MG, Gaillard S, Lanau N, Rouard M, Périn C (January 2008). "GreenPhylDB: a database for plant comparative genomics". Nucleic Acids Research. 36 (Database issue): D991-8. doi:10.1093/nar/gkm934. PMC 2238940. PMID 17986457.

harvard.edu

ui.adsabs.harvard.edu

Fang G, Bhardwaj N, Robilotto R, Gerstein MB (March 2010). "Getting started in gene orthology and functional analysis". PLOS Computational Biology. 6 (3): e1000703. Bibcode:2010PLSCB...6E0703F. doi:10.1371/journal.pcbi.1000703. PMC 2845645. PMID 20361041.
COGs: Clusters of Orthologous Groups of proteins
Tatusov RL, Koonin EV, Lipman DJ (October 1997). "A genomic perspective on protein families". Science. 278 (5338): 631–7. Bibcode:1997Sci...278..631T. doi:10.1126/science.278.5338.631. PMID 9381173.
Singh PP, Arora J, Isambert H (July 2015). "Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes". PLOS Computational Biology. 11 (7): e1004394. Bibcode:2015PLSCB..11E4394S. doi:10.1371/journal.pcbi.1004394. PMC 4504502. PMID 26181593.
OrthoMaM
Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJ (November 2007). "OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics". BMC Evolutionary Biology. 7 (1): 241. Bibcode:2007BMCEE...7..241R. doi:10.1186/1471-2148-7-241. PMC 2249597. PMID 18053139.
Nehrt NL, Clark WT, Radivojac P, Hahn MW (June 2011). "Testing the ortholog conjecture with comparative functional genomic data from mammals". PLOS Computational Biology. 7 (6): e1002073. Bibcode:2011PLSCB...7E2073N. doi:10.1371/journal.pcbi.1002073. PMC 3111532. PMID 21695233.
Coulier F, Popovici C, Villet R, Birnbaum D (December 2000). "MetaHox gene clusters". The Journal of Experimental Zoology. 288 (4): 345–51. Bibcode:2000JEZ...288..345C. doi:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y. PMID 11144283.
Larsson TA, Olsson F, Sundstrom G, Lundin LG, Brenner S, Venkatesh B, Larhammar D (June 2008). "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions". BMC Evolutionary Biology. 8 (1): 184. Bibcode:2008BMCEE...8..184L. doi:10.1186/1471-2148-8-184. PMC 2453138. PMID 18578868.
Pollard SL, Holland PW (September 2000). "Evidence for 14 homeobox gene clusters in human genome ancestry". Current Biology. 10 (17): 1059–62. Bibcode:2000CBio...10.1059P. doi:10.1016/S0960-9822(00)00676-X. PMID 10996074. S2CID 32135432.
Mulley JF, Chiu CH, Holland PW (July 2006). "Breakup of a homeobox cluster after genome duplication in teleosts". Proceedings of the National Academy of Sciences of the United States of America. 103 (27): 10369–10372. Bibcode:2006PNAS..10310369M. doi:10.1073/pnas.0600341103. PMC 1502464. PMID 16801555.
Malaguti G, Singh PP, Isambert H (May 2014). "On the retention of gene duplicates prone to dominant deleterious mutations". Theoretical Population Biology. 93: 38–51. Bibcode:2014TPBio..93...38M. doi:10.1016/j.tpb.2014.01.004. PMID 24530892.
Singh PP, Affeldt S, Malaguti G, Isambert H (July 2014). "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". PLOS Computational Biology. 10 (7): e1003754. Bibcode:2014PLSCB..10E3754S. doi:10.1371/journal.pcbi.1003754. PMC 4117431. PMID 25080083.
McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA (January 2014). "Ohnologs are overrepresented in pathogenic copy number mutations". Proceedings of the National Academy of Sciences of the United States of America. 111 (1): 361–6. Bibcode:2014PNAS..111..361M. doi:10.1073/pnas.1309324111. PMC 3890797. PMID 24368850.
Makino T, McLysaght A (May 2010). "Ohnologs in the human genome are dosage balanced and frequently associated with disease". Proceedings of the National Academy of Sciences of the United States of America. 107 (20): 9270–4. Bibcode:2010PNAS..107.9270M. doi:10.1073/pnas.0914697107. PMC 2889102. PMID 20439718.
Glover NM, Redestig H, Dessimoz C (July 2016). "Homoeologs: What Are They and How Do We Infer Them?". Trends in Plant Science. 21 (7). Cell Press: 609–621. Bibcode:2016TPS....21..609G. doi:10.1016/j.tplants.2016.02.005. PMC 4920642. PMID 27021699.

roundup.hms.harvard.edu

Roundup
Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP (August 2006). "Roundup: a multi-genome repository of orthologs and evolutionary distances". Bioinformatics. 22 (16): 2044–6. doi:10.1093/bioinformatics/btl286. PMID 16777906.

jstor.org

Fitch WM (June 1970). "Distinguishing homologous from analogous proteins". Systematic Zoology. 19 (2): 99–113. doi:10.2307/2412448. JSTOR 2412448. PMID 5449325. Where the homology is the result of gene duplication so that both copies have descended side by side during the history of an organism (for example, a and b hemoglobin) the genes should be called paralogous (para = in parallel). Where the homology is the result of speciation so that the history of the gene reflects the history of the species (for example a hemoglobin in man and mouse) the genes should be called orthologous (ortho = exact).

nih.gov

pubmed.ncbi.nlm.nih.gov

Koonin EV (2005). "Orthologs, paralogs, and evolutionary genomics". Annual Review of Genetics. 39: 309–38. doi:10.1146/annurev.genet.39.073003.114725. PMID 16285863.
Reeck GR, de Haën C, Teller DC, Doolittle RF, Fitch WM, Dickerson RE, et al. (August 1987). ""Homology" in proteins and nucleic acids: a terminology muddle and a way out of it". Cell. 50 (5): 667. doi:10.1016/0092-8674(87)90322-9. PMID 3621342. S2CID 42949514.
Fitch WM (June 1970). "Distinguishing homologous from analogous proteins". Systematic Zoology. 19 (2): 99–113. doi:10.2307/2412448. JSTOR 2412448. PMID 5449325. Where the homology is the result of gene duplication so that both copies have descended side by side during the history of an organism (for example, a and b hemoglobin) the genes should be called paralogous (para = in parallel). Where the homology is the result of speciation so that the history of the gene reflects the history of the species (for example a hemoglobin in man and mouse) the genes should be called orthologous (ortho = exact).
Falciatore A, Merendino L, Barneche F, Ceol M, Meskauskiene R, Apel K, Rochaix JD (January 2005). "The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas". Genes & Development. 19 (1): 176–87. doi:10.1101/gad.321305. PMC 540235. PMID 15630026.
Fang G, Bhardwaj N, Robilotto R, Gerstein MB (March 2010). "Getting started in gene orthology and functional analysis". PLOS Computational Biology. 6 (3): e1000703. Bibcode:2010PLSCB...6E0703F. doi:10.1371/journal.pcbi.1000703. PMC 2845645. PMID 20361041.
COGs: Clusters of Orthologous Groups of proteins
Tatusov RL, Koonin EV, Lipman DJ (October 1997). "A genomic perspective on protein families". Science. 278 (5338): 631–7. Bibcode:1997Sci...278..631T. doi:10.1126/science.278.5338.631. PMID 9381173.
Correia K, Yu SM, Mahadevan R (January 2019). "AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution". Database. 2019. doi:10.1093/database/baz022. PMC 6425859. PMID 30893420.
eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. (January 2010). "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations". Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. (January 2014). "eggNOG v4.0: nested orthology inference across 3686 organisms". Nucleic Acids Research. 42 (Database issue): D231-9. doi:10.1093/nar/gkt1253. PMC 3964997. PMID 24297252.
GreenPhylDB
Conte MG, Gaillard S, Lanau N, Rouard M, Périn C (January 2008). "GreenPhylDB: a database for plant comparative genomics". Nucleic Acids Research. 36 (Database issue): D991-8. doi:10.1093/nar/gkm934. PMC 2238940. PMID 17986457.
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, et al. (January 2011). "GreenPhylDB v2.0: comparative and functional genomics in plants". Nucleic Acids Research. 39 (Database issue): D1095-102. doi:10.1093/nar/gkq811. PMC 3013755. PMID 20864446.
Inparanoid: Eukaryotic Ortholog Groups
Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, et al. (January 2010). "InParanoid 7: new algorithms and tools for eukaryotic orthology analysis". Nucleic Acids Research. 38 (Database issue): D196-203. doi:10.1093/nar/gkp931. PMC 2808972. PMID 19892828.
Sonnhammer EL, Östlund G (January 2015). "InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic". Nucleic Acids Research. 43 (Database issue): D234-9. doi:10.1093/nar/gku1203. PMC 4383983. PMID 25429972.
Singh PP, Arora J, Isambert H (July 2015). "Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes". PLOS Computational Biology. 11 (7): e1004394. Bibcode:2015PLSCB..11E4394S. doi:10.1371/journal.pcbi.1004394. PMC 4504502. PMID 26181593.
Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D, et al. (January 2018). "The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces". Nucleic Acids Research. 46 (D1): D477 – D485. doi:10.1093/nar/gkx1019. PMC 5753216. PMID 29106550.
Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, et al. (January 2017). "OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs". Nucleic Acids Research. 45 (D1): D744 – D749. doi:10.1093/nar/gkw1119. PMC 5210582. PMID 27899580.
Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, et al. (January 2019). "OrthoInspector 3.0: open portal for comparative genomics". Nucleic Acids Research. 47 (D1): D411 – D418. doi:10.1093/nar/gky1068. PMC 6323921. PMID 30380106.
OrthologID
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R (March 2006). "OrthologID: automation of genome-scale ortholog identification within a parsimony framework". Bioinformatics. 22 (6): 699–707. doi:10.1093/bioinformatics/btk040. PMID 16410324.
Egan M, Lee EK, Chiu JC, Coruzzi G, Desalle R (2009). "Gene orthology assessment with OrthologID". In Posada D (ed.). Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology. Vol. 537. Humana Press. pp. 23–38. doi:10.1007/978-1-59745-251-9_2. ISBN 978-1-59745-251-9. PMID 19378138.
OrthoMaM
Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJ (November 2007). "OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics". BMC Evolutionary Biology. 7 (1): 241. Bibcode:2007BMCEE...7..241R. doi:10.1186/1471-2148-7-241. PMC 2249597. PMID 18053139.
Douzery EJ, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V (July 2014). "OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals". Molecular Biology and Evolution. 31 (7): 1923–8. doi:10.1093/molbev/msu132. PMID 24723423.
Scornavacca C, Belkhir K, Lopez J, Dernat R, Delsuc F, Douzery EJ, Ranwez V (April 2019). "OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes". Molecular Biology and Evolution. 36 (4): 861–862. doi:10.1093/molbev/msz015. PMC 6445298. PMID 30698751.
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Chen F, Mackey AJ, Stoeckert CJ, Roos DS (January 2006). "OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups". Nucleic Acids Research. 34 (Database issue): D363-8. doi:10.1093/nar/gkj123. PMC 1347485. PMID 16381887.
Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, et al. (September 2011). "Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups". Current Protocols in Bioinformatics. Chapter 6 (1): Unit 6.12.1–19. doi:10.1002/0471250953.bi0612s35. ISBN 978-0471250951. PMC 3196566. PMID 21901743.
Roundup
Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP (August 2006). "Roundup: a multi-genome repository of orthologs and evolutionary distances". Bioinformatics. 22 (16): 2044–6. doi:10.1093/bioinformatics/btl286. PMID 16777906.
Cosentino, Salvatore; Iwasaki, Wataru (1 January 2019). "SonicParanoid: fast, accurate and easy orthology inference". Bioinformatics. 35 (1): 149–151. doi:10.1093/bioinformatics/bty631. PMC 6298048. PMID 30032301.
TreeFam: Tree families database
van der Heijden RT, Snel B, van Noort V, Huynen MA (March 2007). "Orthology prediction at scalable resolution by phylogenetic tree analysis". BMC Bioinformatics. 8: 83. doi:10.1186/1471-2105-8-83. PMC 1838432. PMID 17346331.
TreeFam: Tree families database
Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, et al. (January 2008). "TreeFam: 2008 Update". Nucleic Acids Research. 36 (Database issue): D735-40. doi:10.1093/nar/gkm1005. PMC 2238856. PMID 18056084.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A (January 2014). "TreeFam v9: a new website, more species and orthology-on-the-fly". Nucleic Acids Research. 42 (Database issue): D922-5. doi:10.1093/nar/gkt1055. PMC 3965059. PMID 24194607.
OrthoFinder: Orthologs from gene trees
Emms DM, Kelly S (November 2019). "OrthoFinder: phylogenetic orthology inference for comparative genomics". Genome Biology. 20 (1): 238. doi:10.1186/s13059-019-1832-y. PMC 6857279. PMID 31727128.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (February 2009). "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates". Genome Research. 19 (2): 327–35. doi:10.1101/gr.073585.107. PMC 2652215. PMID 19029536.
Thanki AS, Soranzo N, Haerty W, Davey RP (March 2018). "GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline". GigaScience. 7 (3): 1–10. doi:10.1093/gigascience/giy005. PMC 5863215. PMID 29425291.
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, et al. (January 2011). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 39 (Database issue): D38-51. doi:10.1093/nar/gkq1172. PMC 3013733. PMID 21097890.
Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS (May 2006). "Improving the specificity of high-throughput ortholog prediction". BMC Bioinformatics. 7: 270. doi:10.1186/1471-2105-7-270. PMC 1524997. PMID 16729895.
Zakany J, Duboule D (August 2007). "The role of Hox genes during vertebrate limb development". Current Opinion in Genetics & Development. 17 (4): 359–66. doi:10.1016/j.gde.2007.05.011. PMID 17644373.
Studer RA, Robinson-Rechavi M (May 2009). "How confident can we be that orthologs are similar, but paralogs differ?". Trends in Genetics. 25 (5): 210–6. doi:10.1016/j.tig.2009.03.004. PMID 19368988.
Nehrt NL, Clark WT, Radivojac P, Hahn MW (June 2011). "Testing the ortholog conjecture with comparative functional genomic data from mammals". PLOS Computational Biology. 7 (6): e1002073. Bibcode:2011PLSCB...7E2073N. doi:10.1371/journal.pcbi.1002073. PMC 3111532. PMID 21695233.
Noda-Garcia L, Romero Romero ML, Longo LM, Kolodkin-Gal I, Tawfik DS (July 2017). "Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation". EMBO Reports. 18 (7): 1139–1149. doi:10.15252/embr.201743990. PMC 5494520. PMID 28468957.
Lundin LG (April 1993). "Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse". Genomics. 16 (1): 1–19. doi:10.1006/geno.1993.1133. PMID 8486346.
Coulier F, Popovici C, Villet R, Birnbaum D (December 2000). "MetaHox gene clusters". The Journal of Experimental Zoology. 288 (4): 345–51. Bibcode:2000JEZ...288..345C. doi:10.1002/1097-010X(20001215)288:4<345::AID-JEZ7>3.0.CO;2-Y. PMID 11144283.
Ruddle FH, Bentley KL, Murtha MT, Risch N (1994). "Gene loss and gain in the evolution of the vertebrates". Development. 1994: 155–61. doi:10.1242/dev.1994.Supplement.155. PMID 7579516.
Pébusque MJ, Coulier F, Birnbaum D, Pontarotti P (September 1998). "Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution". Molecular Biology and Evolution. 15 (9): 1145–59. doi:10.1093/oxfordjournals.molbev.a026022. PMID 9729879.
Larsson TA, Olsson F, Sundstrom G, Lundin LG, Brenner S, Venkatesh B, Larhammar D (June 2008). "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions". BMC Evolutionary Biology. 8 (1): 184. Bibcode:2008BMCEE...8..184L. doi:10.1186/1471-2148-8-184. PMC 2453138. PMID 18578868.
Pollard SL, Holland PW (September 2000). "Evidence for 14 homeobox gene clusters in human genome ancestry". Current Biology. 10 (17): 1059–62. Bibcode:2000CBio...10.1059P. doi:10.1016/S0960-9822(00)00676-X. PMID 10996074. S2CID 32135432.
Mulley JF, Chiu CH, Holland PW (July 2006). "Breakup of a homeobox cluster after genome duplication in teleosts". Proceedings of the National Academy of Sciences of the United States of America. 103 (27): 10369–10372. Bibcode:2006PNAS..10310369M. doi:10.1073/pnas.0600341103. PMC 1502464. PMID 16801555.
Flajnik MF, Kasahara M (September 2001). "Comparative genomics of the MHC: glimpses into the evolution of the adaptive immune system". Immunity. 15 (3): 351–62. doi:10.1016/S1074-7613(01)00198-4. PMID 11567626.
McLysaght A, Hokamp K, Wolfe KH (June 2002). "Extensive genomic duplication during early chordate evolution". Nature Genetics. 31 (2): 200–4. doi:10.1038/ng884. PMID 12032567. S2CID 8263376.
Wolfe K (May 2000). "Robustness--it's not where you think it is". Nature Genetics. 25 (1): 3–4. doi:10.1038/75560. PMID 10802639. S2CID 85257685.
Singh PP, Affeldt S, Cascone I, Selimoglu R, Camonis J, Isambert H (November 2012). "On the expansion of "dangerous" gene repertoires by whole-genome duplications in early vertebrates". Cell Reports. 2 (5): 1387–98. doi:10.1016/j.celrep.2012.09.034. PMID 23168259.
Malaguti G, Singh PP, Isambert H (May 2014). "On the retention of gene duplicates prone to dominant deleterious mutations". Theoretical Population Biology. 93: 38–51. Bibcode:2014TPBio..93...38M. doi:10.1016/j.tpb.2014.01.004. PMID 24530892.
Singh PP, Affeldt S, Malaguti G, Isambert H (July 2014). "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". PLOS Computational Biology. 10 (7): e1003754. Bibcode:2014PLSCB..10E3754S. doi:10.1371/journal.pcbi.1003754. PMC 4117431. PMID 25080083.
McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA (January 2014). "Ohnologs are overrepresented in pathogenic copy number mutations". Proceedings of the National Academy of Sciences of the United States of America. 111 (1): 361–6. Bibcode:2014PNAS..111..361M. doi:10.1073/pnas.1309324111. PMC 3890797. PMID 24368850.
Makino T, McLysaght A (May 2010). "Ohnologs in the human genome are dosage balanced and frequently associated with disease". Proceedings of the National Academy of Sciences of the United States of America. 107 (20): 9270–4. Bibcode:2010PNAS..107.9270M. doi:10.1073/pnas.0914697107. PMC 2889102. PMID 20439718.
Glover NM, Redestig H, Dessimoz C (July 2016). "Homoeologs: What Are They and How Do We Infer Them?". Trends in Plant Science. 21 (7). Cell Press: 609–621. Bibcode:2016TPS....21..609G. doi:10.1016/j.tplants.2016.02.005. PMC 4920642. PMID 27021699.
García-Moreno J, Mindell DP (December 2000). "Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD". Molecular Biology and Evolution. 17 (12): 1826–32. doi:10.1093/oxfordjournals.molbev.a026283. PMID 11110898.

ncbi.nlm.nih.gov

Falciatore A, Merendino L, Barneche F, Ceol M, Meskauskiene R, Apel K, Rochaix JD (January 2005). "The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas". Genes & Development. 19 (1): 176–87. doi:10.1101/gad.321305. PMC 540235. PMID 15630026.
Fang G, Bhardwaj N, Robilotto R, Gerstein MB (March 2010). "Getting started in gene orthology and functional analysis". PLOS Computational Biology. 6 (3): e1000703. Bibcode:2010PLSCB...6E0703F. doi:10.1371/journal.pcbi.1000703. PMC 2845645. PMID 20361041.
COGs: Clusters of Orthologous Groups of proteins
Tatusov RL, Koonin EV, Lipman DJ (October 1997). "A genomic perspective on protein families". Science. 278 (5338): 631–7. Bibcode:1997Sci...278..631T. doi:10.1126/science.278.5338.631. PMID 9381173.
Correia K, Yu SM, Mahadevan R (January 2019). "AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution". Database. 2019. doi:10.1093/database/baz022. PMC 6425859. PMID 30893420.
eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. (January 2010). "eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations". Nucleic Acids Research. 38 (Database issue): D190-5. doi:10.1093/nar/gkp951. PMC 2808932. PMID 19900971.
Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. (January 2014). "eggNOG v4.0: nested orthology inference across 3686 organisms". Nucleic Acids Research. 42 (Database issue): D231-9. doi:10.1093/nar/gkt1253. PMC 3964997. PMID 24297252.
GreenPhylDB
Conte MG, Gaillard S, Lanau N, Rouard M, Périn C (January 2008). "GreenPhylDB: a database for plant comparative genomics". Nucleic Acids Research. 36 (Database issue): D991-8. doi:10.1093/nar/gkm934. PMC 2238940. PMID 17986457.
Rouard M, Guignon V, Aluome C, Laporte MA, Droc G, Walde C, et al. (January 2011). "GreenPhylDB v2.0: comparative and functional genomics in plants". Nucleic Acids Research. 39 (Database issue): D1095-102. doi:10.1093/nar/gkq811. PMC 3013755. PMID 20864446.
Inparanoid: Eukaryotic Ortholog Groups
Ostlund G, Schmitt T, Forslund K, Köstler T, Messina DN, Roopra S, et al. (January 2010). "InParanoid 7: new algorithms and tools for eukaryotic orthology analysis". Nucleic Acids Research. 38 (Database issue): D196-203. doi:10.1093/nar/gkp931. PMC 2808972. PMID 19892828.
Sonnhammer EL, Östlund G (January 2015). "InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic". Nucleic Acids Research. 43 (Database issue): D234-9. doi:10.1093/nar/gku1203. PMC 4383983. PMID 25429972.
Singh PP, Arora J, Isambert H (July 2015). "Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes". PLOS Computational Biology. 11 (7): e1004394. Bibcode:2015PLSCB..11E4394S. doi:10.1371/journal.pcbi.1004394. PMC 4504502. PMID 26181593.
Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D, et al. (January 2018). "The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces". Nucleic Acids Research. 46 (D1): D477 – D485. doi:10.1093/nar/gkx1019. PMC 5753216. PMID 29106550.
Zdobnov EM, Tegenfeldt F, Kuznetsov D, Waterhouse RM, Simão FA, Ioannidis P, et al. (January 2017). "OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs". Nucleic Acids Research. 45 (D1): D744 – D749. doi:10.1093/nar/gkw1119. PMC 5210582. PMID 27899580.
Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, et al. (January 2019). "OrthoInspector 3.0: open portal for comparative genomics". Nucleic Acids Research. 47 (D1): D411 – D418. doi:10.1093/nar/gky1068. PMC 6323921. PMID 30380106.
OrthoMaM
Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, Douzery EJ (November 2007). "OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics". BMC Evolutionary Biology. 7 (1): 241. Bibcode:2007BMCEE...7..241R. doi:10.1186/1471-2148-7-241. PMC 2249597. PMID 18053139.
Scornavacca C, Belkhir K, Lopez J, Dernat R, Delsuc F, Douzery EJ, Ranwez V (April 2019). "OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes". Molecular Biology and Evolution. 36 (4): 861–862. doi:10.1093/molbev/msz015. PMC 6445298. PMID 30698751.
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Chen F, Mackey AJ, Stoeckert CJ, Roos DS (January 2006). "OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups". Nucleic Acids Research. 34 (Database issue): D363-8. doi:10.1093/nar/gkj123. PMC 1347485. PMID 16381887.
Fischer S, Brunk BP, Chen F, Gao X, Harb OS, Iodice JB, et al. (September 2011). "Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups". Current Protocols in Bioinformatics. Chapter 6 (1): Unit 6.12.1–19. doi:10.1002/0471250953.bi0612s35. ISBN 978-0471250951. PMC 3196566. PMID 21901743.
Cosentino, Salvatore; Iwasaki, Wataru (1 January 2019). "SonicParanoid: fast, accurate and easy orthology inference". Bioinformatics. 35 (1): 149–151. doi:10.1093/bioinformatics/bty631. PMC 6298048. PMID 30032301.
Cosentino, Salvatore; Sriswasdi, Sira; Iwasaki, Wataru (25 July 2024). "SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models". Genome Biology. 25 (1). doi:10.1186/s13059-024-03298-4. PMC 11270883.
TreeFam: Tree families database
van der Heijden RT, Snel B, van Noort V, Huynen MA (March 2007). "Orthology prediction at scalable resolution by phylogenetic tree analysis". BMC Bioinformatics. 8: 83. doi:10.1186/1471-2105-8-83. PMC 1838432. PMID 17346331.
TreeFam: Tree families database
Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, et al. (January 2008). "TreeFam: 2008 Update". Nucleic Acids Research. 36 (Database issue): D735-40. doi:10.1093/nar/gkm1005. PMC 2238856. PMID 18056084.
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A (January 2014). "TreeFam v9: a new website, more species and orthology-on-the-fly". Nucleic Acids Research. 42 (Database issue): D922-5. doi:10.1093/nar/gkt1055. PMC 3965059. PMID 24194607.
OrthoFinder: Orthologs from gene trees
Emms DM, Kelly S (November 2019). "OrthoFinder: phylogenetic orthology inference for comparative genomics". Genome Biology. 20 (1): 238. doi:10.1186/s13059-019-1832-y. PMC 6857279. PMID 31727128.
Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E (February 2009). "EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates". Genome Research. 19 (2): 327–35. doi:10.1101/gr.073585.107. PMC 2652215. PMID 19029536.
Thanki AS, Soranzo N, Haerty W, Davey RP (March 2018). "GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline". GigaScience. 7 (3): 1–10. doi:10.1093/gigascience/giy005. PMC 5863215. PMID 29425291.
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, et al. (January 2011). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research. 39 (Database issue): D38-51. doi:10.1093/nar/gkq1172. PMC 3013733. PMID 21097890.
Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS (May 2006). "Improving the specificity of high-throughput ortholog prediction". BMC Bioinformatics. 7: 270. doi:10.1186/1471-2105-7-270. PMC 1524997. PMID 16729895.
Nehrt NL, Clark WT, Radivojac P, Hahn MW (June 2011). "Testing the ortholog conjecture with comparative functional genomic data from mammals". PLOS Computational Biology. 7 (6): e1002073. Bibcode:2011PLSCB...7E2073N. doi:10.1371/journal.pcbi.1002073. PMC 3111532. PMID 21695233.
Noda-Garcia L, Romero Romero ML, Longo LM, Kolodkin-Gal I, Tawfik DS (July 2017). "Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation". EMBO Reports. 18 (7): 1139–1149. doi:10.15252/embr.201743990. PMC 5494520. PMID 28468957.
Larsson TA, Olsson F, Sundstrom G, Lundin LG, Brenner S, Venkatesh B, Larhammar D (June 2008). "Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions". BMC Evolutionary Biology. 8 (1): 184. Bibcode:2008BMCEE...8..184L. doi:10.1186/1471-2148-8-184. PMC 2453138. PMID 18578868.
Mulley JF, Chiu CH, Holland PW (July 2006). "Breakup of a homeobox cluster after genome duplication in teleosts". Proceedings of the National Academy of Sciences of the United States of America. 103 (27): 10369–10372. Bibcode:2006PNAS..10310369M. doi:10.1073/pnas.0600341103. PMC 1502464. PMID 16801555.
Singh PP, Affeldt S, Malaguti G, Isambert H (July 2014). "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". PLOS Computational Biology. 10 (7): e1003754. Bibcode:2014PLSCB..10E3754S. doi:10.1371/journal.pcbi.1003754. PMC 4117431. PMID 25080083.
McLysaght A, Makino T, Grayton HM, Tropeano M, Mitchell KJ, Vassos E, Collier DA (January 2014). "Ohnologs are overrepresented in pathogenic copy number mutations". Proceedings of the National Academy of Sciences of the United States of America. 111 (1): 361–6. Bibcode:2014PNAS..111..361M. doi:10.1073/pnas.1309324111. PMC 3890797. PMID 24368850.
Makino T, McLysaght A (May 2010). "Ohnologs in the human genome are dosage balanced and frequently associated with disease". Proceedings of the National Academy of Sciences of the United States of America. 107 (20): 9270–4. Bibcode:2010PNAS..107.9270M. doi:10.1073/pnas.0914697107. PMC 2889102. PMID 20439718.
Glover NM, Redestig H, Dessimoz C (July 2016). "Homoeologs: What Are They and How Do We Infer Them?". Trends in Plant Science. 21 (7). Cell Press: 609–621. Bibcode:2016TPS....21..609G. doi:10.1016/j.tplants.2016.02.005. PMC 4920642. PMID 27021699.

nyu.edu

nypg.bio.nyu.edu

OrthologID
Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R (March 2006). "OrthologID: automation of genome-scale ortholog identification within a parsimony framework". Bioinformatics. 22 (6): 699–707. doi:10.1093/bioinformatics/btk040. PMID 16410324.

orthomcl.org

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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scu.edu

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semanticscholar.org

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inparanoid.sbc.su.se

Inparanoid: Eukaryotic Ortholog Groups
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treefam.org

TreeFam: Tree families database
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TreeFam: Tree families database
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unil.ch

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zenodo.org

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COGs: Clusters of Orthologous Groups of proteins
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