{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,24]],"date-time":"2026-01-24T19:45:36Z","timestamp":1769283936177,"version":"3.49.0"},"reference-count":26,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2013,9,26]],"date-time":"2013-09-26T00:00:00Z","timestamp":1380153600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003223","type":"journal-article","created":{"date-parts":[[2013,9,26]],"date-time":"2013-09-26T17:13:18Z","timestamp":1380215598000},"page":"e1003223","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":34,"title":["Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs"],"prefix":"10.1371","volume":"9","author":[{"given":"Stephen A.","family":"Smith","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph W.","family":"Brown","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cody E.","family":"Hinchliff","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2013,9,26]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/sysbio\/46.3.523","article-title":"Gene Trees in Species Trees","volume":"46","author":"WP Maddison","year":"1997","journal-title":"Systematic Biology"},{"key":"ref2","unstructured":"Page RDM (2002) Tangled Trees: Phylogeny, Cospeciation, and Coevolution. University Of Chicago Press, 378 pp."},{"key":"ref3","unstructured":"Knowles LL, Kubatko LS, editors (2010) Estimating Species Trees: Practical and Theoretical Aspects. Wiley-Blackwell, 232 pp."},{"key":"ref4","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1093\/molbev\/msj030","article-title":"Application of phylogenetic networks in evolutionary studies","volume":"23","author":"DH Huson","year":"2006","journal-title":"Molecular Biology and Evolution"},{"key":"ref5","doi-asserted-by":"crossref","unstructured":"Bininda-Emonds OR, editor (2004) Phylogenetic supertrees: Combining information to reveal the Tree of Life (Computational Biology). Springer, 564 pp.","DOI":"10.1007\/978-1-4020-2330-9"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1080\/10635150590946961","article-title":"Analysis and visualization of tree space","volume":"54","author":"DM Hillis","year":"2005","journal-title":"Systematic Biology"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1080\/10635150701485091","article-title":"Summarizing a posterior distribution of trees using agreement subtrees","volume":"56","author":"KA Cranston","year":"2007","journal-title":"Systematic Biology"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1372","DOI":"10.1093\/bioinformatics\/btq110","article-title":"DensiTree: making sense of sets of phylogenetic trees","volume":"26","author":"RR Bouckaert","year":"2010","journal-title":"Bioinformatics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"i248","DOI":"10.1093\/bioinformatics\/btr210","article-title":"Tanglegrams for rooted phylogenetic trees and networks","volume":"27","author":"C Scornavacca","year":"2011","journal-title":"Bioinformatics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1093\/bioinformatics\/btq539","article-title":"BUCKy: gene tree\/species tree reconciliation with Bayesian concordance analysis","volume":"26","author":"BR Larget","year":"2010","journal-title":"Bioinformatics"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/gbe\/evq077","article-title":"A survey of combinatorial methods for phylogenetic networks","volume":"3","author":"DH Huson","year":"2011","journal-title":"Genome biology and evolution"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1016\/S0169-5347(97)01242-1","article-title":"Phylogenetic supertrees: Assembling the trees of life","volume":"13","author":"MJ Sanderson","year":"1998","journal-title":"Trends in Ecology & Evolution"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1756-0500-3-95","article-title":"The Supertree Tool Kit","volume":"3","author":"KE Davis","year":"2010","journal-title":"BMC Research Notes"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/nature05634","article-title":"The delayed rise of present-day mammals","volume":"446","author":"ORP Bininda-Emonds","year":"2007","journal-title":"Nature"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"1904","DOI":"10.1073\/pnas.0308127100","article-title":"Darwin&apos;s abominable mystery: Insights from a supertree of the angiosperms","volume":"101","author":"TJ Davies","year":"2004","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1752","DOI":"10.1093\/molbev\/msm095","article-title":"Supertrees disentangle the chimerical origin of eukaryotic genomes","volume":"24","author":"D Pisani","year":"2007","journal-title":"Molecular Biology and Evolution"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1080\/10635150590950362","article-title":"Measuring support and finding unsupportedrelationships in supertrees","volume":"54","author":"M Wilkinson","year":"2005","journal-title":"Systematic Biology"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1093\/sysbio\/sys090","article-title":"Amalgamating source trees with different taxonomic levels","volume":"62","author":"V Berry","year":"2013","journal-title":"Systematic biology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"444","DOI":"10.1038\/nature11631","article-title":"The global diversity of birds in space and time","volume":"491","author":"W Jetz","year":"2012","journal-title":"Nature"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"14689","DOI":"10.1073\/pnas.0305199101","article-title":"Local graph alignment and motif search in biological networks","volume":"101","author":"J Berg","year":"2004","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1039\/c2ib00140c","article-title":"C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks","volume":"4","author":"V Memi\u0161evi\u0107","year":"2012","journal-title":"Integrative biology quantitative biosciences from nano to macro"},{"key":"ref22","first-page":"1","article-title":"Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm","author":"A L\u00f6ytynoja","year":"2012","journal-title":"Bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"704","DOI":"10.3732\/ajb.1000404","article-title":"Angiosperm phylogeny: 17 genes, 640 taxa","volume":"98","author":"DE Soltis","year":"2011","journal-title":"American Journal of Botany"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1890\/11-0638.1","article-title":"Synthesizing phylogenetic knowledge for ecological research","volume":"93","author":"J Beaulieu","year":"2012","journal-title":"Ecology"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.1126\/science.1157704","article-title":"A phylogenomic study of birds reveals their evolutionary history","volume":"320","author":"SJ Hackett","year":"2008","journal-title":"Science"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1093\/sysbio\/sys062","article-title":"Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks","volume":"61","author":"DH Huson","year":"2012","journal-title":"Systematic Biology"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003223","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,7,25]],"date-time":"2019-07-25T20:50:16Z","timestamp":1564087816000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003223"}},"subtitle":[],"editor":[{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2013,9,26]]},"references-count":26,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2013,9,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003223","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,9,26]]}}}