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To facilitate this research, OrthoVenn3 has been developed as a powerful, web-based tool that enables users to efficiently identify and annotate orthologous clusters and infer phylogenetic relationships across a range of species. The latest upgrade of OrthoVenn includes several important new features, including enhanced orthologous cluster identification accuracy, improved visualization capabilities for numerous sets of data, and wrapped phylogenetic analysis. Furthermore, OrthoVenn3 now provides gene family contraction and expansion analysis to support researchers better understanding the evolutionary history of gene families, as well as collinearity analysis to detect conserved and variable genomic structures. With its intuitive user interface and robust functionality, OrthoVenn3 is a valuable resource for comparative genomics research. The tool is freely accessible at https:\/\/orthovenn3.bioinfotoolkits.net.<\/jats:p>","DOI":"10.1093\/nar\/gkad313","type":"journal-article","created":{"date-parts":[[2023,4,28]],"date-time":"2023-04-28T13:34:45Z","timestamp":1682688885000},"page":"W397-W403","source":"Crossref","is-referenced-by-count":461,"title":["OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes"],"prefix":"10.1093","volume":"51","author":[{"given":"Jiahe","family":"Sun","sequence":"first","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University , Chongqing , China"}]},{"given":"Fang","family":"Lu","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University , Chongqing , China"}]},{"given":"Yongjiang","family":"Luo","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University , Chongqing , China"}]},{"given":"Lingzi","family":"Bie","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University , Chongqing , China"}]},{"given":"Ling","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University , Beijing , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4706-8171","authenticated-orcid":false,"given":"Yi","family":"Wang","sequence":"additional","affiliation":[{"name":"Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University , Chongqing , China"}]}],"member":"286","published-online":{"date-parts":[[2023,4,28]]},"reference":[{"key":"2023070504582469400_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giy013","article-title":"10KP: a phylodiverse genome sequencing plan","volume":"7","author":"Cheng","year":"2018","journal-title":"Gigascience"},{"key":"2023070504582469400_B2","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/522034d","article-title":"Genomics: bird sequencing project takes off","volume":"522","author":"Zhang","year":"2015","journal-title":"Nature"},{"key":"2023070504582469400_B3","doi-asserted-by":"crossref","first-page":"1311","DOI":"10.1126\/science.1251385","article-title":"Comparative genomics reveals insights into avian genome evolution and adaptation","volume":"346","author":"Zhang","year":"2014","journal-title":"Science"},{"key":"2023070504582469400_B4","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1126\/science.287.5461.2204","article-title":"Comparative genomics of the eukaryotes","volume":"287","author":"Rubin","year":"2000","journal-title":"Science"},{"key":"2023070504582469400_B5","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/nature01262","article-title":"Initial sequencing and comparative analysis of the mouse genome","volume":"420","author":"Waterston","year":"2002","journal-title":"Nature"},{"key":"2023070504582469400_B6","doi-asserted-by":"crossref","first-page":"W78","DOI":"10.1093\/nar\/gkv487","article-title":"OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023070504582469400_B7","doi-asserted-by":"crossref","first-page":"W52","DOI":"10.1093\/nar\/gkz333","article-title":"OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species","volume":"47","author":"Xu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023070504582469400_B8","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","article-title":"OrthoFinder: phylogenetic orthology inference for comparative genomics","volume":"20","author":"Emms","year":"2019","journal-title":"Genome Biol."},{"key":"2023070504582469400_B9","doi-asserted-by":"crossref","first-page":"1983","DOI":"10.1109\/TVCG.2014.2346248","article-title":"UpSet: visualization of intersecting sets","volume":"20","author":"Lex","year":"2014","journal-title":"IEEE Trans. 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