{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:52:46Z","timestamp":1740135166438,"version":"3.37.3"},"reference-count":73,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,7,22]],"date-time":"2019-07-22T00:00:00Z","timestamp":1563753600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,7,22]],"date-time":"2019-07-22T00:00:00Z","timestamp":1563753600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"German research foundation","doi-asserted-by":"crossref","award":["MU 2875\/3-1"],"award-info":[{"award-number":["MU 2875\/3-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Open Access Publication Fund of the University of M\u00fcnster","award":["N\/A"],"award-info":[{"award-number":["N\/A"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-2982-3","type":"journal-article","created":{"date-parts":[[2019,7,22]],"date-time":"2019-07-22T13:03:26Z","timestamp":1563800606000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface"],"prefix":"10.1186","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4443-7733","authenticated-orcid":false,"given":"Ben C.","family":"St\u00f6ver","sequence":"first","affiliation":[]},{"given":"Sarah","family":"Wiechers","sequence":"additional","affiliation":[]},{"given":"Kai F.","family":"M\u00fcller","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,7,22]]},"reference":[{"key":"2982_CR1","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1525\/bio.2009.59.7.12","volume":"59","author":"S Kelling","year":"2009","unstructured":"Kelling S, Hochachka WM, Fink D, Riedewald M, Caruana R, Ballard G, et al. Data-intensive science: a new paradigm for biodiversity studies. BioScience. 2009;59:613\u201320.","journal-title":"BioScience."},{"key":"2982_CR2","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.tree.2011.11.016","volume":"27","author":"WK Michener","year":"2012","unstructured":"Michener WK, Jones MB. Ecoinformatics: supporting ecology as a data-intensive science. Trends Ecol Evol. 2012;27:85\u201393.","journal-title":"Trends Ecol Evol"},{"key":"2982_CR3","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.1038","volume":"6","author":"MR McKain","year":"2018","unstructured":"McKain MR, Johnson MG, Uribe-Convers S, Eaton D, Yang Y. Practical considerations for plant phylogenomics. Appl Plant Sci. 2018;6:e1038.","journal-title":"Appl Plant Sci"},{"key":"2982_CR4","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1139\/gen-2015-0185","volume":"59","author":"MF Geiger","year":"2016","unstructured":"Geiger MF, Astrin JJ, Borsch T, Burkhardt U, Grobe P, Hand R, et al. How to tackle the molecular species inventory for an industrialized nation - lessons from the first phase of the German barcode of life initiative GBOL (2012\u20132015). Genome. 2016;59:661\u201370.","journal-title":"Genome."},{"key":"2982_CR5","doi-asserted-by":"crossref","unstructured":"Ratnasingham S, Hebert PDN. Bold: the barcode of life data system (\n                    http:\/\/www.barcodinglife.org\n                    \n                  ). Mol Ecol Notes 2007;7:355\u2013364.","DOI":"10.1111\/j.1471-8286.2007.01678.x"},{"key":"2982_CR6","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1111\/j.1471-8286.2007.01670.x","volume":"7","author":"KC Kerr","year":"2007","unstructured":"Kerr KC, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PD. Comprehensive DNA barcode coverage of north American birds. Mol Ecol Resour. 2007;7:535\u201343.","journal-title":"Mol Ecol Resour"},{"key":"2982_CR7","unstructured":"Global Plants on JSTOR. \n                    https:\/\/plants.jstor.org\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3897\/zookeys.209.3699","volume":"209","author":"V Smith","year":"2012","unstructured":"Smith V, Blagoderov V. Bringing collections out of the dark. ZooKeys. 2012;209:1\u20136.","journal-title":"ZooKeys."},{"key":"2982_CR9","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1146\/annurev-ecolsys-102209-144636","volume":"41","author":"JL Dickinson","year":"2010","unstructured":"Dickinson JL, Zuckerberg B, Bonter DN. Citizen science as an ecological research tool: challenges and benefits. Annu Rev Ecol Evol Syst. 2010;41:149\u201372.","journal-title":"Annu Rev Ecol Evol Syst"},{"key":"2982_CR10","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1016\/j.tree.2011.11.006","volume":"27","author":"WM Hochachka","year":"2012","unstructured":"Hochachka WM, Fink D, Hutchinson RA, Sheldon D, Wong W-K, Kelling S. Data-intensive science applied to broad-scale citizen science. Trends Ecol Evol. 2012;27:130\u20137.","journal-title":"Trends Ecol Evol"},{"key":"2982_CR11","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1016\/j.ecoinf.2013.07.006","volume":"23","author":"A Joly","year":"2014","unstructured":"Joly A, Go\u00ebau H, Bonnet P, Baki\u0107 V, Barbe J, Selmi S, et al. Interactive plant identification based on social image data. Ecol Inform. 2014;23:22\u201334.","journal-title":"Ecol Inform"},{"key":"2982_CR12","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.ecoser.2017.09.017","volume":"28","author":"M Schr\u00f6ter","year":"2017","unstructured":"Schr\u00f6ter M, Kraemer R, Mantel M, Kabisch N, Hecker S, Richter A, et al. Citizen science for assessing ecosystem services: status, challenges and opportunities. Ecosyst Serv. 2017;28:80\u201394.","journal-title":"Ecosyst Serv"},{"key":"2982_CR13","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1186\/1756-0500-5-574","volume":"5","author":"A Stoltzfus","year":"2012","unstructured":"Stoltzfus A, O\u2019Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, et al. Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes. 2012;5:574.","journal-title":"BMC Res Notes"},{"key":"2982_CR14","unstructured":"Rambaut A. TreeThief: a tool for manual phylogenetic tree entry from scanned images. Department of Zoology, University of Oxford. Oxford. Available from: http:\/\/microbe. bio. indiana. edu; 1999"},{"key":"2982_CR15","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1186\/1471-2105-12-178","volume":"12","author":"J Hughes","year":"2011","unstructured":"Hughes J. TreeRipper web application: towards a fully automated optical tree recognition software. BMC Bioinformatics. 2011;12:178.","journal-title":"BMC Bioinformatics."},{"key":"2982_CR16","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1186\/1471-2105-13-110","volume":"13","author":"T Laubach","year":"2012","unstructured":"Laubach T, von Haeseler A, Lercher MJ. TreeSnatcher plus: capturing phylogenetic trees from images. BMC Bioinformatics. 2012;13:110.","journal-title":"BMC Bioinformatics"},{"key":"2982_CR17","doi-asserted-by":"publisher","unstructured":"Murray-Rust P, Smith-Unna R, Mounce R. AMI-diagram: mining facts from images. -Lib Mag. 2014;20 11\/12. doi:\n                    https:\/\/doi.org\/10.1045\/november14-murray-rust  \n                    \n                  .","DOI":"10.1045\/november14-murray-rust"},{"key":"2982_CR18","doi-asserted-by":"publisher","unstructured":"Cranston K, Harmon LJ, O\u2019Leary MA, Lisle C. Best practices for data sharing in phylogenetic research. PLOS Curr Tree Life. 2014. \n                    https:\/\/doi.org\/10.1371\/currents.tol.bf01eff4a6b60ca4825c69293dc59645  \n                    \n                  .","DOI":"10.1371\/currents.tol.bf01eff4a6b60ca4825c69293dc59645"},{"key":"2982_CR19","doi-asserted-by":"crossref","unstructured":"Poisot TE, Mounce R, Gravel D. Moving toward a sustainable ecological science: don\u2019t let data go to waste! Ideas Ecol Evol. 2013;6.","DOI":"10.4033\/iee.2013.6b.14.f"},{"key":"2982_CR20","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1016\/j.tree.2011.11.001","volume":"27","author":"CS Parr","year":"2012","unstructured":"Parr CS, Guralnick R, Cellinese N, Page RDM. Evolutionary informatics: unifying knowledge about the diversity of life. Trends Ecol Evol. 2012;27:94\u2013103.","journal-title":"Trends Ecol Evol"},{"key":"2982_CR21","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1186\/1471-2148-14-66","volume":"14","author":"A Kenall","year":"2014","unstructured":"Kenall A, Harold S, Foote C. An open future for ecological and evolutionary data? BMC Evol Biol. 2014;14:66.","journal-title":"BMC Evol Biol"},{"key":"2982_CR22","unstructured":"Piel WH, Chan L, Dominus MJ, Ruan J, Vos RA, Tannen V. TreeBASE v. 2: a database of phylogenetic knowledge. In: e-BioSphere 2009. London; 2009. \n                    https:\/\/treebase.org\/\n                    \n                  . Accessed 28 Feb 2017"},{"key":"2982_CR23","unstructured":"National Evolutionary Synthesis Center, UNC-CH Metadata Research Center, Oxford University, The British Library. Dryad. Dryad. \n                    https:\/\/datadryad.org\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR24","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/1471-2105-14-158","volume":"14","author":"A Stoltzfus","year":"2013","unstructured":"Stoltzfus A, Lapp H, Matasci N, Deus H, Sidlauskas B, Zmasek CM, et al. Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. BMC Bioinformatics. 2013;14:158.","journal-title":"BMC Bioinformatics."},{"key":"2982_CR25","doi-asserted-by":"publisher","first-page":"12764","DOI":"10.1073\/pnas.1423041112","volume":"112","author":"CE Hinchliff","year":"2015","unstructured":"Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proc Natl Acad Sci. 2015;112:12764\u20139.","journal-title":"Proc Natl Acad Sci"},{"key":"2982_CR26","doi-asserted-by":"publisher","first-page":"1812","DOI":"10.1093\/molbev\/msx116","volume":"34","author":"S Kumar","year":"2017","unstructured":"Kumar S, Stecher G, Suleski M, Hedges SB. TimeTree: a resource for timelines, Timetrees, and divergence times. Mol Biol Evol. 2017;34:1812\u20139.","journal-title":"Mol Biol Evol"},{"key":"2982_CR27","doi-asserted-by":"publisher","unstructured":"White EP, Baldridge E, Brym ZT, Locey KJ, McGlinn DJ, Supp SR. Nine simple ways to make it easier to (re) use your data. Ideas Ecol Evol. 2013;6. \n                    https:\/\/doi.org\/10.4033\/iee.v6i2.4608  \n                    \n                  .","DOI":"10.4033\/iee.v6i2.4608"},{"key":"2982_CR28","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.tree.2010.11.006","volume":"26","author":"MC Whitlock","year":"2011","unstructured":"Whitlock MC. Data archiving in ecology and evolution: best practices. Trends Ecol Evol. 2011;26:61\u20135.","journal-title":"Trends Ecol Evol"},{"key":"2982_CR29","doi-asserted-by":"publisher","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","volume":"40","author":"S Federhen","year":"2012","unstructured":"Federhen S. The NCBI taxonomy database. Nucleic Acids Res. 2012;40:D136\u201343.","journal-title":"Nucleic Acids Res"},{"key":"2982_CR30","doi-asserted-by":"publisher","first-page":"bav094","DOI":"10.1093\/database\/bav094","volume":"2015","author":"N Kilian","year":"2015","unstructured":"Kilian N, Henning T, Plitzner P, M\u00fcller A, G\u00fcntsch A, St\u00f6ver BC, et al. Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens. Database. 2015;2015:bav094.","journal-title":"Database."},{"key":"2982_CR31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003285","volume":"9","author":"GK Sandve","year":"2013","unstructured":"Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten simple rules for reproducible computational research. PLoS Comput Biol. 2013;9:e1003285.","journal-title":"PLoS Comput Biol"},{"key":"2982_CR32","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1089\/omi.2006.10.231","volume":"10","author":"J Leebens-Mack","year":"2006","unstructured":"Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, et al. Taking the first steps towards a standard for reporting on phylogenies: minimum information about a phylogenetic analysis (MIAPA). OMICS J Integr Biol. 2006;10:231\u20137.","journal-title":"OMICS J Integr Biol"},{"key":"2982_CR33","volume-title":"Working Notes of CLEF 2016 conference","author":"ST Hang","year":"2016","unstructured":"Hang ST, Tatsuma A, Aono M. Bluefield (kde tut) at lifeclef 2016 plant identification task. In: Working Notes of CLEF 2016 conference; 2016. \n                    http:\/\/ceur-ws.org\/Vol-1609\/16090459.pdf\n                    \n                  . Accessed 14 Sep 2016."},{"key":"2982_CR34","doi-asserted-by":"publisher","first-page":"3305","DOI":"10.1073\/pnas.1524473113","volume":"113","author":"P Wilf","year":"2016","unstructured":"Wilf P, Zhang S, Chikkerur S, Little SA, Wing SL, Serre T. Computer vision cracks the leaf code. Proc Natl Acad Sci. 2016;113:3305\u201310.","journal-title":"Proc Natl Acad Sci"},{"key":"2982_CR35","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1016\/j.ecoinf.2017.05.005","volume":"40","author":"P Barr\u00e9","year":"2017","unstructured":"Barr\u00e9 P, St\u00f6ver BC, M\u00fcller KF, Steinhage V. LeafNet: a computer vision system for automatic plant species identification. Ecol Inform. 2017;40:50\u20136.","journal-title":"Ecol Inform."},{"key":"2982_CR36","volume-title":"Phylip input files","author":"J Felsenstein","year":"2013","unstructured":"Felsenstein J. Phylip input files. 2013. \n                    http:\/\/evolution.genetics.washington.edu\/phylip\/doc\/main.html#inputfiles\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR37","unstructured":"Felsenstein J. The Newick tree format. 1993. \n                    http:\/\/evolution.genetics.washington.edu\/phylip\/newicktree.html\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR38","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1093\/sysbio\/46.4.590","volume":"46","author":"DR Maddison","year":"1997","unstructured":"Maddison DR, Swofford D, Maddison WP. NEXUS: an extensible file format for systematic information. Syst Biol. 1997;46:590\u2013621.","journal-title":"Syst Biol"},{"key":"2982_CR39","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1093\/sysbio\/sys025","volume":"61","author":"RA Vos","year":"2012","unstructured":"Vos RA, Balhoff JP, Caravas JA, Holder MT, Lapp H, Maddison WP, et al. NeXML: rich, extensible, and verifiable representation of comparative data and metadata. Syst Biol. 2012;61:675\u201389.","journal-title":"Syst Biol"},{"key":"2982_CR40","doi-asserted-by":"publisher","first-page":"356","DOI":"10.1186\/1471-2105-10-356","volume":"10","author":"MV Han","year":"2009","unstructured":"Han MV, Zmasek CM. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics. 2009;10:356.","journal-title":"BMC Bioinformatics."},{"key":"2982_CR41","unstructured":"RDF - Semantic Web Standards. \n                    https:\/\/www.w3.org\/RDF\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR42","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1038\/nbt1139","volume":"23","author":"X Wang","year":"2005","unstructured":"Wang X, Gorlitsky R, Almeida JS. From XML to RDF: how semantic web technologies will change the design of \u201comic\u201d standards. Nat Biotechnol. 2005;23:1099\u2013103.","journal-title":"Nat Biotechnol"},{"key":"2982_CR43","volume-title":"Design patterns. Elements of reusable object-oriented software","author":"E Gamma","year":"1994","unstructured":"Gamma E, Helm R, Johnson RE, Vlissides J. Design patterns. Elements of reusable object-oriented software. 1st ed. Reprint. Reading, Mass: Prentice Hall; 1994.","edition":"1"},{"key":"2982_CR44","unstructured":"Miller M, Schwartz T, Pfeiffer W. Relaxed PHYLIP format. Relaxed PHYLIP format documentation at CIPRES. 2016. \n                    http:\/\/www.phylo.org\/index.php\/help\/relaxed_phylip\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR45","unstructured":"Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. 2016. \n                    http:\/\/mesquiteproject.org\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR46","unstructured":"Ronquist F, Teslenko M, van der Mark P, Larget B, Donald S, Huelsenbeck J. The MrBayes Input Format. 2016. \n                    http:\/\/mrbayes.sourceforge.net\/Help\/format.html\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR47","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/sysbio\/sys029","volume":"61","author":"F Ronquist","year":"2012","unstructured":"Ronquist F, Teslenko M, van der MP, Ayres DL, Darling A, H\u00f6hna S, et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012;61:539\u201342.","journal-title":"Syst Biol"},{"key":"2982_CR48","doi-asserted-by":"crossref","unstructured":"Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016:msw054.","DOI":"10.1093\/molbev\/msw054"},{"key":"2982_CR49","doi-asserted-by":"publisher","first-page":"532","DOI":"10.1186\/1471-2105-9-532","volume":"9","author":"G Cardona","year":"2008","unstructured":"Cardona G, Rossell\u00f3 F, Valiente G. Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinformatics. 2008;9:532.","journal-title":"BMC Bioinformatics."},{"key":"2982_CR50","unstructured":"M\u00fcller J, M\u00fcller K, Neinhuis C, Quandt D. PhyDE - Phylogenetic Data Editor. 2006. \n                    http:\/\/phyde.de\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR51","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/1471-2105-11-7","volume":"11","author":"BC St\u00f6ver","year":"2010","unstructured":"St\u00f6ver BC, M\u00fcller KF. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics. 2010;11:7.","journal-title":"BMC Bioinformatics."},{"key":"2982_CR52","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1093\/bioinformatics\/17.4.383","volume":"17","author":"CM Zmasek","year":"2001","unstructured":"Zmasek CM, Eddy SR. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics. 2001;17:383\u20134.","journal-title":"Bioinformatics."},{"key":"2982_CR53","unstructured":"Zmasek CM. NHX - New Hampshire eXtended, version 2.0. 2014. \n                    https:\/\/sites.google.com\/site\/cmzmasek\/home\/software\/forester\/nhx\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR54","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003537","volume":"10","author":"R Bouckaert","year":"2014","unstructured":"Bouckaert R, Heled J, K\u00fchnert D, Vaughan T, Wu C-H, Xie D, et al. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol. 2014;10:e1003537.","journal-title":"PLoS Comput Biol"},{"key":"2982_CR55","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1080\/14772000.2013.818588","volume":"11","author":"L Vogt","year":"2013","unstructured":"Vogt L. eScience and the need for data standards in the life sciences: in pursuit of objectivity rather than truth. Syst Biodivers. 2013;11:257\u201370.","journal-title":"Syst Biodivers"},{"key":"2982_CR56","unstructured":"Zmasek CM. forester: Software libraries for evolutionary biology and comparative genomics research. 2015. \n                    https:\/\/sites.google.com\/site\/cmzmasek\/home\/software\/forester\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR57","doi-asserted-by":"crossref","unstructured":"Maddison DR, Schulz K-S, Maddison WP. The tree of life web project. Zootaxa. 2007;1668 Linnaeus Tercentenary: Progress in Invertebrate Taxonomy:19\u201340.","DOI":"10.11646\/zootaxa.1668.1.4"},{"key":"2982_CR58","doi-asserted-by":"publisher","first-page":"2693","DOI":"10.1093\/bioinformatics\/bts494","volume":"28","author":"A Prli\u0107","year":"2012","unstructured":"Prli\u0107 A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, et al. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012;28:2693\u20135.","journal-title":"Bioinformatics."},{"key":"2982_CR59","doi-asserted-by":"publisher","first-page":"2096","DOI":"10.1093\/bioinformatics\/btn397","volume":"24","author":"RCG Holland","year":"2008","unstructured":"Holland RCG, Down TA, Pocock M, Prlic A, Huen D, James K, et al. BioJava: an open-source framework for bioinformatics. Bioinformatics. 2008;24:2096\u20137.","journal-title":"Bioinformatics."},{"key":"2982_CR60","volume-title":"Balhoff J","author":"RA Vos","year":"2016","unstructured":"Vos RA, Huang D, Midford PE. Balhoff J. Sukumaran J. nexml.java - Java API for NeXML. GitHub: Holder MT; 2016. \n                    https:\/\/github.com\/nexml\/nexml.java\n                    \n                  . Accessed 18 Jun 2019"},{"issue":"1","key":"2982_CR61","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1186\/1471-2105-8-191","volume":"8","author":"Thomas Hladish","year":"2007","unstructured":"Hladish T, Gopalan V, Liang C, Qiu W, Yang P, Stoltzfus A. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics. 2007;8(1).","journal-title":"BMC Bioinformatics"},{"key":"2982_CR62","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1111\/2041-210X.12469","volume":"7","author":"C Boettiger","year":"2016","unstructured":"Boettiger C, Chamberlain S, Vos R, Lapp H. RNeXML: a package for reading and writing richly annotated phylogenetic, character and trait data in r. Methods Ecol Evol. 2016;7:352\u20137.","journal-title":"Methods Ecol Evol"},{"key":"2982_CR63","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1101\/gr.361602","volume":"12","author":"JE Stajich","year":"2002","unstructured":"Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12:1611\u20138.","journal-title":"Genome Res"},{"key":"2982_CR64","doi-asserted-by":"publisher","first-page":"2330","DOI":"10.1093\/bioinformatics\/btg319","volume":"19","author":"PO Lewis","year":"2003","unstructured":"Lewis PO. NCL: a C++ class library for interpreting data files in NEXUS format. Bioinformatics. 2003;19:2330\u20131.","journal-title":"Bioinformatics."},{"key":"2982_CR65","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.1093\/bioinformatics\/btq228","volume":"26","author":"J Sukumaran","year":"2010","unstructured":"Sukumaran J, Holder MT. DendroPy: a Python library for phylogenetic computing. Bioinformatics. 2010;26:1569\u201371.","journal-title":"Bioinformatics."},{"key":"2982_CR66","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/1471-2105-12-63","volume":"12","author":"RA Vos","year":"2011","unstructured":"Vos RA, Caravas J, Hartmann K, Jensen MA, Miller C. BIO::Phylo-phyloinformatic analysis using perl. BMC Bioinformatics. 2011;12:63.","journal-title":"BMC Bioinformatics."},{"key":"2982_CR67","unstructured":"Py4J - A Bridge between Python and Java. \n                    https:\/\/www.py4j.org\/index.html\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR68","unstructured":"rJava - Low-level R to Java interface. \n                    https:\/\/www.rforge.net\/rJava\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR69","doi-asserted-by":"crossref","unstructured":"St\u00f6ver BC, M\u00fcller KF. LibrAlign: a GUI library for displaying and editing multiple sequence alignments and attached data. 2016. \n                    http:\/\/bioinfweb.info\/LibrAlign\/\n                    \n                  . Accessed 18 Jun 2019.","DOI":"10.1007\/s15005-016-1925-z"},{"key":"2982_CR70","unstructured":"Berendsohn WG. Devising the EDIT platform for Cybertaxonomy. In: Tools for identifying biodiversity: Progress and problems. Proceedings of the international congress, Paris, September 20\u201322, 2010. EUT Edizioni Universit\u00e0 di Trieste; 2010. \n                    http:\/\/www.openstarts.units.it\/dspace\/handle\/10077\/3737\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR71","unstructured":"St\u00f6ver BC, M\u00fcller KF. AlignmentComparator: an application to efficiently visualize and annotate differences between alternative multiple sequence alignments. 2014. \n                    http:\/\/bioinfweb.info\/AlignmentComparator\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR72","unstructured":"St\u00f6ver BC, Bohn J, van Groen S, K\u00f6sters L, Quandt D, M\u00fcller KF. PhyDE 2 - an alignment editor for phylogenetic purposes. PhyDE 2 - an alignment editor for phylogenetic purposes. 2019. \n                    http:\/\/bioinfweb.info\/PhyDE2\/\n                    \n                  . Accessed 18 Jun 2019."},{"key":"2982_CR73","unstructured":"Preston-Werner T. Semantic Versioning 2.0.0. 2013. \n                    https:\/\/semver.org\/\n                    \n                  . Accessed 18 Jun 2019."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2982-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-2982-3\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-2982-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T23:06:32Z","timestamp":1595286392000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-2982-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,7,22]]},"references-count":73,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["2982"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-2982-3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2019,7,22]]},"assertion":[{"value":"17 May 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 July 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 July 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"402"}}