{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T20:17:53Z","timestamp":1774469873243,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010686","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,11,21]],"date-time":"2022-11-21T00:00:00Z","timestamp":1668988800000}}],"reference-count":20,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T00:00:00Z","timestamp":1667952000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["ANR-15-IDEX-01"],"award-info":[{"award-number":["ANR-15-IDEX-01"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018695","name":"AgreenSkills","doi-asserted-by":"publisher","award":["609398"],"award-info":[{"award-number":["609398"]}],"id":[{"id":"10.13039\/501100018695","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present\n                    <jats:italic>AvP<\/jats:italic>\n                    which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1010686","type":"journal-article","created":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T14:07:57Z","timestamp":1668002877000},"page":"e1010686","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":30,"title":["AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3406-3715","authenticated-orcid":true,"given":"Georgios D.","family":"Koutsovoulos","sequence":"first","affiliation":[]},{"given":"Sol\u00e8ne","family":"Granjeon Noriot","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6032-1127","authenticated-orcid":true,"given":"Marc","family":"Bailly-Bechet","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4146-5608","authenticated-orcid":true,"given":"Etienne G. J.","family":"Danchin","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9355-5491","authenticated-orcid":true,"given":"Corinne","family":"Rancurel","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,11,9]]},"reference":[{"issue":"1","key":"pcbi.1010686.ref001","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1186\/s12915-016-0330-x","article-title":"Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?","volume":"14","author":"EGJ Danchin","year":"2016","journal-title":"BMC Biology"},{"issue":"1","key":"pcbi.1010686.ref002","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"C Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"issue":"5880","key":"pcbi.1010686.ref003","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1126\/science.1156407","article-title":"Massive Horizontal Gene Transfer in Bdelloid Rotifers","volume":"320","author":"EA Gladyshev","year":"2008","journal-title":"Science"},{"issue":"11","key":"pcbi.1010686.ref004","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pgen.1003035","article-title":"Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers","volume":"8","author":"C Boschetti","year":"2012","journal-title":"PLOS Genetics"},{"issue":"16","key":"pcbi.1010686.ref005","doi-asserted-by":"crossref","first-page":"2975","DOI":"10.1016\/j.cell.2022.06.014","article-title":"HGT is widespread in insects and contributes to male courtship in lepidopterans","volume":"185","author":"Y Li","year":"2022","journal-title":"Cell"},{"issue":"18","key":"pcbi.1010686.ref006","doi-asserted-by":"crossref","first-page":"5053","DOI":"10.1073\/pnas.1600338113","article-title":"No evidence for extensive horizontal gene transfer in the genome of the tardigrade Hypsibius dujardini","volume":"113","author":"G Koutsovoulos","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"13","key":"pcbi.1010686.ref007","doi-asserted-by":"crossref","first-page":"2056","DOI":"10.1093\/bioinformatics\/btw105","article-title":"ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony","volume":"32","author":"E Jacox","year":"2016","journal-title":"Bioinformatics"},{"issue":"5","key":"pcbi.1010686.ref008","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1093\/bioinformatics\/btw686","article-title":"Xenolog classification","volume":"33","author":"CA Darby","year":"2016","journal-title":"Bioinformatics"},{"issue":"1","key":"pcbi.1010686.ref009","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"B Buchfink","year":"2015","journal-title":"Nature Methods"},{"issue":"1","key":"pcbi.1010686.ref010","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":"DM Emms","year":"2019","journal-title":"Genome Biology"},{"issue":"4","key":"pcbi.1010686.ref011","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Molecular Biology and Evolution"},{"issue":"15","key":"pcbi.1010686.ref012","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","author":"S Capella-Guti\u00e9rrez","year":"2009","journal-title":"Bioinformatics"},{"issue":"3","key":"pcbi.1010686.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014Approximately Maximum-Likelihood Trees for Large Alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PLOS ONE"},{"issue":"5","key":"pcbi.1010686.ref014","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era","volume":"37","author":"BQ Minh","year":"2020","journal-title":"Molecular Biology and Evolution"},{"issue":"2","key":"pcbi.1010686.ref015","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1093\/molbev\/msx302","article-title":"Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets","volume":"35","author":"X Zhou","year":"2018","journal-title":"Molecular Biology and Evolution"},{"key":"pcbi.1010686.ref016","unstructured":"Rambaut A. 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