{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:00Z","timestamp":1772138040252,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T00:00:00Z","timestamp":1596153600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Priority Program","award":["SPP-1596 MA5082\/7-1"],"award-info":[{"award-number":["SPP-1596 MA5082\/7-1"]}]},{"name":"Collaborative Research Centre 1076 AquaDiva"},{"DOI":"10.13039\/100012957","name":"Friedrich Schiller University Jena","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012957","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004807","name":"DFG","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>PoSeiDon is an easy-to-use pipeline that helps researchers to find recombination events and sites under positive selection in protein-coding sequences. By entering homologous sequences, PoSeiDon builds an alignment, estimates a best-fitting substitution model and performs a recombination analysis followed by the construction of all corresponding phylogenies. Finally, significantly positive selected sites are detected according to different models for the full alignment and possible recombination fragments. The results of PoSeiDon are summarized in a user-friendly HTML page providing all intermediate results and the graphical representation of recombination events and positively selected sites.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PoSeiDon is freely available at https:\/\/github.com\/hoelzer\/poseidon. The pipeline is implemented in Nextflow with Docker support and processes the output of various tools.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa695","type":"journal-article","created":{"date-parts":[[2020,7,24]],"date-time":"2020-07-24T07:32:22Z","timestamp":1595575942000},"page":"1018-1020","source":"Crossref","is-referenced-by-count":13,"title":["PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection"],"prefix":"10.1093","volume":"37","author":[{"given":"Martin","family":"H\u00f6lzer","sequence":"first","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science , Jena 07743, Germany"},{"name":"European Virus Bioinformatics Center, Friedrich Schiller University Jena , Jena 07743, Germany"}]},{"given":"Manja","family":"Marz","sequence":"additional","affiliation":[{"name":"RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science , Jena 07743, Germany"},{"name":"European Virus Bioinformatics Center, Friedrich Schiller University Jena , Jena 07743, Germany"},{"name":"FLI Leibniz Institute for Age Research , Marz Associated Research Group, Jena 07745, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,7,31]]},"reference":[{"key":"2023051612150153500_btaa695-B1","doi-asserted-by":"crossref","first-page":"W7","DOI":"10.1093\/nar\/gkq291","article-title":"TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations","volume":"38","author":"Abascal","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023051612150153500_btaa695-B2","doi-asserted-by":"crossref","first-page":"2455","DOI":"10.1093\/bioinformatics\/btq429","article-title":"Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology","volume":"26","author":"Delport","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051612150153500_btaa695-B3","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"Di Tommaso","year":"2017","journal-title":"Nat. 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