{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T19:08:06Z","timestamp":1775329686392,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,1]],"date-time":"2018-06-01T00:00:00Z","timestamp":1527811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Carl Tryggers Stiftelse and Uppsala University"},{"DOI":"10.13039\/501100009252","name":"Science for Life Laboratory","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009252","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Phylogenomic datasets invariably contain undetected stretches of non-homologous characters due to poor-quality sequences or erroneous gene models. The large-scale multi-gene nature of these datasets renders impractical or impossible detailed manual curation of sequences, but few tools exist that can automate this task. To address this issue, we developed a new method that takes as input a set of unaligned homologous sequences and uses an explicit probabilistic approach to identify and mask regions with non-homologous adjacent characters. These regions are defined as sharing no statistical support for homology with any other sequence in the set, which can result from e.g. sequencing errors or gene prediction errors creating frameshifts. Our methodology is implemented in the program PREQUAL, which is a fast and accurate tool for high-throughput filtering of sequences. The program is primarily aimed at amino acid sequences, although it can handle protein coding DNA sequences as well. It is fully customizable to allow fine-tuning of the filtering sensitivity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The program PREQUAL is written in C\/C++\u2009and available through a GNU GPL v3.0 at https:\/\/github.com\/simonwhelan\/prequal.<\/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\/bty448","type":"journal-article","created":{"date-parts":[[2018,5,30]],"date-time":"2018-05-30T11:20:10Z","timestamp":1527679210000},"page":"3929-3930","source":"Crossref","is-referenced-by-count":132,"title":["PREQUAL: detecting non-homologous characters in sets of unaligned homologous sequences"],"prefix":"10.1093","volume":"34","author":[{"given":"Simon","family":"Whelan","sequence":"first","affiliation":[{"name":"Department of Evolutionary Genetics, Program in Evolutionary Biology, Uppsala University, Uppsala, Sweden"}]},{"given":"Iker","family":"Irisarri","sequence":"additional","affiliation":[{"name":"Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8248-8462","authenticated-orcid":false,"given":"Fabien","family":"Burki","sequence":"additional","affiliation":[{"name":"Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden"},{"name":"Science for Life Laboratory, Uppsala University, Uppsala, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2018,6,1]]},"reference":[{"key":"2023012712340103200_bty448-B1","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/nature12027","article-title":"The African coelacanth genome provides insights into tetrapod evolution","volume":"496","author":"Amemiya","year":"2013","journal-title":"Nature"},{"key":"2023012712340103200_bty448-B2","doi-asserted-by":"crossref","first-page":"20152802","DOI":"10.1098\/rspb.2015.2802","article-title":"Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista","volume":"283","author":"Burki","year":"2016","journal-title":"Proc. R. Soc. B"},{"key":"2023012712340103200_bty448-B3","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511790492","author":"Durbin","year":"1998","journal-title":"Biological sequence analysis: probabilistic models of proteins and nucleic acids"},{"key":"2023012712340103200_bty448-B4","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1093\/sysbio\/syw057","article-title":"The identification of the closest living relative(s) of tetrapods: phylogenomic lessons for resolving short ancient internodes","volume":"65","author":"Irisarri","year":"2016","journal-title":"Syst. Biol."},{"key":"2023012712340103200_bty448-B5","doi-asserted-by":"crossref","first-page":"3699","DOI":"10.3109\/19401736.2015.1079863","article-title":"The complete mitochondrial genomes of the Gal\u00e1pagos iguanas, Amblyrhynchus cristatus and Conolophus subcristatus","volume":"27","author":"MacLeod","year":"2016","journal-title":"Mitochondrial DNA"},{"key":"2023012712340103200_bty448-B7","doi-asserted-by":"crossref","first-page":"1737","DOI":"10.1038\/s41559-017-0331-3","article-title":"Ctenophore relationships and their placement as the sister group to all other animals","volume":"1","author":"Whelan","year":"2017","journal-title":"Nat. Ecol. Evol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3929\/48920073\/bioinformatics_34_22_3929.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3929\/48920073\/bioinformatics_34_22_3929.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:23:29Z","timestamp":1674825809000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/22\/3929\/5026659"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,1]]},"references-count":6,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2018,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty448","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,11,15]]},"published":{"date-parts":[[2018,6,1]]}}}