{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,3]],"date-time":"2023-10-03T09:55:03Z","timestamp":1696326903653},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"S13","license":[{"start":{"date-parts":[[2012,8,1]],"date-time":"2012-08-01T00:00:00Z","timestamp":1343779200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/dna.cs.byu.edu\/psoda\" ext-link-type=\"uri\">http:\/\/dna.cs.byu.edu\/psoda<\/jats:ext-link>\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-s13-s8","type":"journal-article","created":{"date-parts":[[2019,12,11]],"date-time":"2019-12-11T01:59:55Z","timestamp":1576029595000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Phylogenetic search through partial tree mixing"],"prefix":"10.1186","volume":"13","author":[{"given":"Kenneth","family":"Sundberg","sequence":"first","affiliation":[]},{"given":"Mark","family":"Clement","sequence":"additional","affiliation":[]},{"given":"Quinn","family":"Snell","sequence":"additional","affiliation":[]},{"given":"Dan","family":"Ventura","sequence":"additional","affiliation":[]},{"given":"Michael","family":"Whiting","sequence":"additional","affiliation":[]},{"given":"Keith","family":"Crandall","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,8,24]]},"reference":[{"key":"5293_CR1","first-page":"296","volume-title":"Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005)","author":"B Chor","year":"2005","unstructured":"Chor B, Tuller T: Maximum Likelihood of Evolutionary Trees is Hard. In Proceedings of the 9th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2005). Volume 3500. Springer; 2005:296\u2013310. 10.1007\/11415770_23"},{"issue":"5310","key":"5293_CR2","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1126\/science.276.5310.227","volume":"276","author":"J Huelsenbeck","year":"1997","unstructured":"Huelsenbeck J, Rannala B: Phylogenetic Methods Come of Age: Testing Hypotheses in an Evolutionary Context. Science 1997, 276(5310):227. 10.1126\/science.276.5310.227","journal-title":"Science"},{"key":"5293_CR3","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1007\/978-3-642-04241-6_27","volume-title":"Proceedings of Algorithms in Bioinformatics: 9th International Workshop (WABI 2009)","author":"K Sundberg","year":"2009","unstructured":"Sundberg K, Clement M, Snell Q: Visualizing Phylogenetic Treespace Using Cartographic Projections. In Proceedings of Algorithms in Bioinformatics: 9th International Workshop (WABI 2009). Springer; 2009:321."},{"key":"5293_CR4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00026-001-8006-8","volume":"5","author":"B Allen","year":"2001","unstructured":"Allen B, Steel M: Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees. Annals of Combinatorics 2001, 5: 1\u201315. 10.1007\/s00026-001-8006-8","journal-title":"Annals of Combinatorics"},{"issue":"2","key":"5293_CR5","doi-asserted-by":"publisher","first-page":"130","DOI":"10.2307\/2406046","volume":"11","author":"C Michener","year":"1957","unstructured":"Michener C, Sokal R: A Quantitative Approach to a Problem in Classification. Evolution 1957, 11(2):130\u2013162. 10.2307\/2406046","journal-title":"Evolution"},{"issue":"4","key":"5293_CR6","first-page":"406","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou N, Nei M: The Neighbor-Joining Method: a New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution 1987, 4(4):406.","journal-title":"Molecular Biology and Evolution"},{"key":"5293_CR7","first-page":"12","volume":"50","author":"M Li","year":"2004","unstructured":"Li M, Chen X, Li X, Ma B, Vit\u00e1nyi P: The Similarity Metric. IEEE Transactions on Information Theory 2004, 50: 12.","journal-title":"IEEE Transactions on Information Theory"},{"issue":"1-2","key":"5293_CR8","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","volume":"53","author":"D Robinson","year":"1981","unstructured":"Robinson D, Foulds L: Comparison of Phylogenetic Trees. Mathematical Biosciences 1981, 53(1\u20132):131\u2013147. 10.1016\/0025-5564(81)90043-2","journal-title":"Mathematical Biosciences"},{"key":"5293_CR9","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4899-6846-3","volume-title":"Introduction to Computational Biology: Maps, Sequences and Genomes","author":"M Waterman","year":"1995","unstructured":"Waterman M: Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman & Hall\/CRC; 1995."},{"key":"5293_CR10","doi-asserted-by":"crossref","unstructured":"Sundberg K, Clement M, Snell Q: On the use of cartographic projections in visualizing phylo-genetic tree space. Algorithms Mol Biol 2010., 5(26):","DOI":"10.1186\/1748-7188-5-26"},{"issue":"6","key":"5293_CR11","doi-asserted-by":"publisher","first-page":"724","DOI":"10.1089\/cmb.2007.R012","volume":"14","author":"N Pattengale","year":"2007","unstructured":"Pattengale N, Gottlieb E, Moret B: Efficiently Computing the Robinson-Foulds Metric. Journal of Computational Biology 2007, 14(6):724\u2013735. 10.1089\/cmb.2007.R012","journal-title":"Journal of Computational Biology"},{"issue":"4","key":"5293_CR12","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1111\/j.1096-0031.1999.tb00277.x","volume":"15","author":"K Nixon","year":"1999","unstructured":"Nixon K: The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis. Cladistics 1999, 15(4):407\u2013414. 10.1111\/j.1096-0031.1999.tb00277.x","journal-title":"Cladistics"},{"key":"5293_CR13","volume-title":"PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4","author":"D Swofford","year":"2003","unstructured":"Swofford D: PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. Sunderland, Massachusetts: Sinauer Associates; 2003."},{"issue":"5","key":"5293_CR14","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1111\/j.1096-0031.2008.00217.x","volume":"24","author":"P Goloboff","year":"2008","unstructured":"Goloboff P, Farris J, Nixon K: TNT, a Free Program for Phylogenetic Analysis. Cladistics 2008, 24(5):774\u2013786. 10.1111\/j.1096-0031.2008.00217.x","journal-title":"Cladistics"},{"issue":"3-4","key":"5293_CR15","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1089\/106652799318337","volume":"6","author":"D Huson","year":"1999","unstructured":"Huson D, Nettles S, Warnow T: Disk-covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction. Journal of Computational Biology 1999, 6(3\u20134):369\u2013386. 10.1089\/106652799318337","journal-title":"Journal of Computational Biology"},{"issue":"4","key":"5293_CR16","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1111\/j.1096-0031.1999.tb00278.x","volume":"15","author":"P Goloboff","year":"1999","unstructured":"Goloboff P: Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima. Cladistics 1999, 15(4):415\u2013428. 10.1111\/j.1096-0031.1999.tb00278.x","journal-title":"Cladistics"},{"key":"5293_CR17","first-page":"74","volume-title":"Proceedings of the 4th Biotechnology and Bioinformatics Symposium (BIOT-07)","author":"H Carroll","year":"2007","unstructured":"Carroll H, Ebbert M, Clement M, Snell Q: PSODA: Better Tasting and Less Filling Than PAUP. Proceedings of the 4th Biotechnology and Bioinformatics Symposium (BIOT-07) 2007, 74\u201378."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S13-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-13-S13-S8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S13-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T19:37:05Z","timestamp":1630525025000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S13-S8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,8]]},"references-count":17,"journal-issue":{"issue":"S13","published-print":{"date-parts":[[2012,8]]}},"alternative-id":["5293"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s13-s8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,8]]},"assertion":[{"value":"24 August 2012","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S8"}}