{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T01:52:33Z","timestamp":1781229153514,"version":"3.54.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,20]],"date-time":"2022-12-20T00:00:00Z","timestamp":1671494400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 Research and Innovation Program","award":["833522"],"award-info":[{"award-number":["833522"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny analyses. Here, we present syntenet, an R package to infer and analyze synteny networks from whole-genome protein sequence data. The package offers a simple and complete framework, including data preprocessing, synteny detection and network inference, network clustering and phylogenomic profiling, and microsynteny-based phylogeny inference. Graphical functions are also available to create publication-ready plots. Synteny networks inferred with syntenet can highlight taxon-specific gene clusters that likely contributed to the evolution of important traits, and microsynteny-based phylogenies can help resolve phylogenetic relationships under debate.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>syntenet is available on Bioconductor (https:\/\/bioconductor.org\/packages\/syntenet), and the source code is available on a GitHub repository (https:\/\/github.com\/almeidasilvaf\/syntenet).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac806","type":"journal-article","created":{"date-parts":[[2022,12,20]],"date-time":"2022-12-20T19:29:09Z","timestamp":1671564549000},"source":"Crossref","is-referenced-by-count":27,"title":["syntenet: an R\/Bioconductor package for the inference and analysis of synteny networks"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5314-2964","authenticated-orcid":false,"given":"Fabricio","family":"Almeida-Silva","sequence":"first","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology, VIB , 9052 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Zhao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Stress Biology for Arid Areas\/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University , Yangling 712100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristian K","family":"Ullrich","sequence":"additional","affiliation":[{"name":"Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology , Ploen 24306, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6777-6565","authenticated-orcid":false,"given":"M Eric","family":"Schranz","sequence":"additional","affiliation":[{"name":"Biosystematics Group, Wageningen University and Research , Wageningen 6708, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent, Belgium"},{"name":"VIB Center for Plant Systems Biology, VIB , 9052 Ghent, Belgium"},{"name":"Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria , Pretoria 0028, South Africa"},{"name":"College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing 210095, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,20]]},"reference":[{"key":"2023010805390260000_btac806-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023010805390260000_btac806-B2","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1038\/s41592-021-01101-x","article-title":"Sensitive protein alignments at tree-of-life scale using DIAMOND","volume":"18","author":"Buchfink","year":"2021","journal-title":"Nat. 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