{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T03:11:35Z","timestamp":1761621095472,"version":"3.41.0"},"reference-count":17,"publisher":"Association for Computing Machinery (ACM)","issue":"1","license":[{"start":{"date-parts":[[2012,1,1]],"date-time":"2012-01-01T00:00:00Z","timestamp":1325376000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"name":"research group PABI","award":["BO 1910\/5"],"award-info":[{"award-number":["BO 1910\/5"]}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":["ACM Trans. Algorithms"],"published-print":{"date-parts":[[2012,1]]},"abstract":"<jats:p>\n            In computational phylogenetics, the problem of constructing a consensus tree for a given set of rooted input trees has frequently been addressed. In this article we study the\n            <jats:sc>Minimum-Flip Problem<\/jats:sc>\n            : the input trees are transformed into a binary matrix, and we want to find a perfect phylogeny for this matrix using a minimum number of flips, that is, corrections of single entries in the matrix. The graph-theoretical formulation of the problem is as follows: Given a bipartite graph\n            <jats:italic>G<\/jats:italic>\n            = (\n            <jats:italic>Vt<\/jats:italic>\n            \u222a\n            <jats:italic>Vc<\/jats:italic>\n            ,\n            <jats:italic>E<\/jats:italic>\n            ), the task is to find a minimum set of edge modifications such that the resulting graph has no induced path with four edges that starts and ends in\n            <jats:italic>Vt<\/jats:italic>\n            , where\n            <jats:italic>Vt<\/jats:italic>\n            corresponds to the taxa set and\n            <jats:italic>Vc<\/jats:italic>\n            corresponds to the character set.\n          <\/jats:p>\n          <jats:p>\n            We present two fixed-parameter algorithms for the\n            <jats:sc>Minimum-Flip Problem<\/jats:sc>\n            , one with running time\n            <jats:italic>O<\/jats:italic>\n            (4.83\n            <jats:italic>k<\/jats:italic>\n            +\n            <jats:italic>poly<\/jats:italic>\n            (\n            <jats:italic>m<\/jats:italic>\n            ,\n            <jats:italic>n<\/jats:italic>\n            )) and another one with running time\n            <jats:italic>O<\/jats:italic>\n            (4.42\n            <jats:italic>k<\/jats:italic>\n            +\n            <jats:italic>poly<\/jats:italic>\n            (\n            <jats:italic>m<\/jats:italic>\n            ,\n            <jats:italic>n<\/jats:italic>\n            )) for\n            <jats:italic>n<\/jats:italic>\n            taxa,\n            <jats:italic>m<\/jats:italic>\n            characters,\n            <jats:italic>k<\/jats:italic>\n            flips, and\n            <jats:italic>poly<\/jats:italic>\n            (\n            <jats:italic>m<\/jats:italic>\n            ,\n            <jats:italic>n<\/jats:italic>\n            ) denotes a polynomial function in\n            <jats:italic>m<\/jats:italic>\n            and\n            <jats:italic>n<\/jats:italic>\n            . Additionally, we discuss several heuristic improvements. We also report computational results on phylogenetic data.\n          <\/jats:p>","DOI":"10.1145\/2071379.2071386","type":"journal-article","created":{"date-parts":[[2012,1,24]],"date-time":"2012-01-24T16:47:14Z","timestamp":1327423634000},"page":"1-17","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Improved Fixed-Parameter Algorithms for Minimum-Flip Consensus Trees"],"prefix":"10.1145","volume":"8","author":[{"given":"Sebastian","family":"B\u00f6cker","sequence":"first","affiliation":[{"name":"Friedrich-Schiller-Universit\u00e4t Jena"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Quang Bao Anh","family":"Bui","sequence":"additional","affiliation":[{"name":"Friedrich-Schiller-Universit\u00e4t Jena"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anke","family":"Truss","sequence":"additional","affiliation":[{"name":"Friedrich-Schiller-Universit\u00e4t Jena"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2012,1]]},"reference":[{"key":"e_1_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.2307\/2412432"},{"volume-title":"2004","author":"Bininda-Emonds O. R.","key":"e_1_2_1_2_1","unstructured":"Bininda-Emonds , O. R. , Ed. 2004 . Phylogenetic Supertrees : Combining Information to Reveal the Tree of Life. Computational Biology Book Series, vol. 4 , Kluwer Academic , Dordrecht, the Netherlands. Bininda-Emonds, O. R., Ed. 2004. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Computational Biology Book Series, vol. 4, Kluwer Academic, Dordrecht, the Netherlands."},{"key":"e_1_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1006\/aama.1995.1020"},{"key":"e_1_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1016\/0020-0190(96)00050-6"},{"key":"e_1_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1177\/117693430600200003"},{"key":"e_1_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2006.26"},{"key":"e_1_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/0025-5564(86)90161-6"},{"key":"e_1_2_1_8_1","doi-asserted-by":"crossref","unstructured":"Downey R. G. and Fellows M. R. 1999. Parameterized Complexity. Springer. Downey R. G. and Fellows M. R. 1999. Parameterized Complexity . Springer.","DOI":"10.1007\/978-1-4612-0515-9"},{"key":"e_1_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.5555\/320176.320229"},{"key":"e_1_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00453-004-1090-5"},{"key":"e_1_2_1_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/net.3230210104"},{"volume-title":"Proceedings of the Symposium on Discrete Algorithms (SODA\u201995)","author":"Kannan S.","key":"e_1_2_1_12_1","unstructured":"Kannan , S. , Warnow , T. , and Yooseph , S . 1995. Computing the local consensus of trees . In Proceedings of the Symposium on Discrete Algorithms (SODA\u201995) . 68--77. Kannan, S., Warnow, T., and Yooseph, S. 1995. Computing the local consensus of trees. In Proceedings of the Symposium on Discrete Algorithms (SODA\u201995). 68--77."},{"volume-title":"Proceedings of the Foundations of Software Technology and Theoretical Computer Science (FSTTCS\u201908)","author":"Komusiewicz C.","key":"e_1_2_1_13_1","unstructured":"Komusiewicz , C. and Uhlmann , J . 2008. A cubic-vertex kernel for flip consensus tree . In Proceedings of the Foundations of Software Technology and Theoretical Computer Science (FSTTCS\u201908) . Leibniz International Proceedings in Informatics. 280--291. Komusiewicz, C. and Uhlmann, J. 2008. A cubic-vertex kernel for flip consensus tree. In Proceedings of the Foundations of Software Technology and Theoretical Computer Science (FSTTCS\u201908). Leibniz International Proceedings in Informatics. 280--291."},{"key":"e_1_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/0166-218X(95)00074-2"},{"volume-title":"Invitation to Fixed-Parameter Algorithms","author":"Niedermeier R.","key":"e_1_2_1_15_1","unstructured":"Niedermeier , R. 2006. Invitation to Fixed-Parameter Algorithms . Oxford University Press . Niedermeier, R. 2006. Invitation to Fixed-Parameter Algorithms. Oxford University Press."},{"key":"e_1_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0020-0190(00)00004-1"},{"key":"e_1_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-218X(00)00202-X"}],"container-title":["ACM Transactions on Algorithms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2071379.2071386","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/2071379.2071386","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T10:06:22Z","timestamp":1750241182000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/2071379.2071386"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1]]},"references-count":17,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,1]]}},"alternative-id":["10.1145\/2071379.2071386"],"URL":"https:\/\/doi.org\/10.1145\/2071379.2071386","relation":{},"ISSN":["1549-6325","1549-6333"],"issn-type":[{"type":"print","value":"1549-6325"},{"type":"electronic","value":"1549-6333"}],"subject":[],"published":{"date-parts":[[2012,1]]},"assertion":[{"value":"2008-11-01","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2009-07-01","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2012-01-01","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}