{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:44Z","timestamp":1772138084816,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,24]],"date-time":"2017-11-24T00:00:00Z","timestamp":1511481600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend these approaches and to facilitate their integration into analysis pipelines, there is a need for robust, open-source implementations of associated data structures and algorithms. Here, we present SPECTRE, a readily available, open-source library of data structures written in Java, that comes complete with new implementations of several pre-published algorithms and a basic interactive graphical interface for visualizing planar split networks. SPECTRE also supports the use of longer running algorithms by providing command line interfaces, which can be executed on servers or in High Performance Computing environments.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n Full source code is available under the GPLv3 license at: https:\/\/github.com\/maplesond\/SPECTRE. SPECTRE\u2019s core library is available from Maven Central at: https:\/\/mvnrepository.com\/artifact\/uk.ac.uea.cmp.spectre\/core. Documentation is available at: http:\/\/spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io\/en\/latest\/<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx740","type":"journal-article","created":{"date-parts":[[2017,11,23]],"date-time":"2017-11-23T15:16:26Z","timestamp":1511450186000},"page":"1056-1057","source":"Crossref","is-referenced-by-count":7,"title":["SPECTRE: a suite of phylogenetic tools for reticulate evolution"],"prefix":"10.1093","volume":"34","author":[{"given":"Sarah","family":"Bastkowski","sequence":"first","affiliation":[{"name":"Earlham Institute, Norwich Research Park, Norwich, UK"}]},{"given":"Daniel","family":"Mapleson","sequence":"additional","affiliation":[{"name":"Earlham Institute, Norwich Research Park, Norwich, UK"}]},{"given":"Andreas","family":"Spillner","sequence":"additional","affiliation":[{"name":"Merseburg University of Applied Sciences, Merseburg, Germany"}]},{"given":"Taoyang","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Computing Sciences, University of East Anglia, Norwich, UK"}]},{"given":"Monika","family":"Balvo\u010di\u016bt\u0117","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of T\u00fcbingen, Sand 14, T\u00fcbingen, Germany"}]},{"given":"Vincent","family":"Moulton","sequence":"additional","affiliation":[{"name":"School of Computing Sciences, University of East Anglia, Norwich, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,11,24]]},"reference":[{"key":"2023012712470833400_btx740-B1","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1093\/sysbio\/syu001","article-title":"FlatNJ: a novel network-based approach to visualize evolutionary and biogeographical relationships","volume":"63","author":"Balvo\u010di\u016bt\u0117","year":"2014","journal-title":"Syst. Biol"},{"key":"2023012712470833400_btx740-B2","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/1055-7903(92)90021-8","article-title":"Split decomposition: a new and useful approach to phylogenetic analysis of distance data","volume":"1","author":"Bandelt","year":"1992","journal-title":"Mol. Phylogenet. Evol"},{"key":"2023012712470833400_btx740-B3","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ipl.2013.10.003","article-title":"Fishing for minimum evolution trees with NeighborNets","volume":"114","author":"Bastkowski","year":"2014","journal-title":"Inform. Process. Lett"},{"key":"2023012712470833400_btx740-B4","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1007\/BF02198834","article-title":"Recombination between sequences of hepatitis B virus from different genotypes","volume":"42","author":"Bollyky","year":"1996","journal-title":"J. Mol. 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Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1056\/48913994\/bioinformatics_34_6_1056.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/6\/1056\/48913994\/bioinformatics_34_6_1056.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:39:43Z","timestamp":1674808783000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/6\/1056\/4657069"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,11,24]]},"references-count":10,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2018,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx740","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/169177","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,3,15]]},"published":{"date-parts":[[2017,11,24]]}}}