{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,6]],"date-time":"2025-04-06T21:40:08Z","timestamp":1743975608139,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":40,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642315183"},{"type":"electronic","value":"9783642315190"}],"license":[{"start":{"date-parts":[[2013,1,1]],"date-time":"2013-01-01T00:00:00Z","timestamp":1356998400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2013,1,1]],"date-time":"2013-01-01T00:00:00Z","timestamp":1356998400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013]]},"DOI":"10.1007\/978-3-642-31519-0_12","type":"book-chapter","created":{"date-parts":[[2012,8,13]],"date-time":"2012-08-13T14:30:13Z","timestamp":1344868213000},"page":"189-203","source":"Crossref","is-referenced-by-count":6,"title":["Maximum Parsimony Phylogenetic Inference Using Simulated Annealing"],"prefix":"10.1007","author":[{"given":"Jean-Michel","family":"Richer","sequence":"first","affiliation":[]},{"given":"Eduardo","family":"Rodriguez-Tello","sequence":"additional","affiliation":[]},{"given":"Karla E.","family":"Vazquez-Ortiz","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"12_CR1","first-page":"193","volume":"40","author":"E.H.L. Aarts","year":"1985","unstructured":"Aarts, E.H.L., Van Laarhoven, P.J.M.: Statistical cooling: A general approach to combinatorial optimization problems. Philips Journal of Research\u00a040, 193\u2013226 (1985)","journal-title":"Philips Journal of Research"},{"issue":"1","key":"12_CR2","first-page":"1","volume":"16","author":"D. Abramson","year":"1999","unstructured":"Abramson, D., Krishnamoorthy, M., Dang, H.: Simulated annealing cooling schedules for the school timetabling problem. Asia-Pacific Journal of Operational Research\u00a016(1), 1\u201322 (1999)","journal-title":"Asia-Pacific Journal of Operational Research"},{"issue":"1","key":"12_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00026-001-8006-8","volume":"5","author":"B.J. Allen","year":"2001","unstructured":"Allen, B.J., Steel, M.: Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Combinatorics\u00a05(1), 1\u201315 (2001)","journal-title":"Annals of Combinatorics"},{"issue":"4","key":"12_CR4","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1023\/A:1015439913121","volume":"8","author":"A. Andreatta","year":"2002","unstructured":"Andreatta, A., Ribeiro, C.C.: Heuristics for the phylogeny problem. Journal of Heuristics\u00a08(4), 429\u2013447 (2002)","journal-title":"Journal of Heuristics"},{"issue":"2","key":"12_CR5","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1093\/bioinformatics\/btg402","volume":"20","author":"D. Barker","year":"2003","unstructured":"Barker, D.: LVB: parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics\u00a020(2), 274\u2013275 (2003)","journal-title":"Bioinformatics"},{"key":"12_CR6","unstructured":"Barker, D.: LVB homepage (2012), http:\/\/biology.st-andrews.ac.uk\/cegg\/lvb.aspx"},{"issue":"3,pt 1","key":"12_CR7","first-page":"233","volume":"19","author":"L.L. Cavalli-Sforza","year":"1967","unstructured":"Cavalli-Sforza, L.L., Edwards, A.W.F.: Phylogenetic analysis. models and estimation procedures. The American Journal of Human Genetics\u00a019(3,pt 1), 233\u2013257 (1967)","journal-title":"The American Journal of Human Genetics"},{"issue":"5","key":"12_CR8","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1109\/52.536462","volume":"13","author":"D.M. Cohen","year":"1996","unstructured":"Cohen, D.M., Dalal, S.R., Parelius, J., Patton, G.C.: The combinatorial design approach to automatic test generation. IEEE Software\u00a013(5), 83\u201388 (1996)","journal-title":"IEEE Software"},{"key":"12_CR9","first-page":"121","volume":"58","author":"C.J. Colbourn","year":"2004","unstructured":"Colbourn, C.J.: Combinatorial aspects of covering arrays. Le Matematiche\u00a058, 121\u2013167 (2004)","journal-title":"Le Matematiche"},{"key":"12_CR10","doi-asserted-by":"crossref","unstructured":"de Landgraaf, W.A., Eiben, A.E., Nannen, V.: Parameter calibration using meta-algorithms. In: Proceedings of the IEEE Congress on Evolutionary Computation, pp. 71\u201378. IEEE Press (2007)","DOI":"10.1109\/CEC.2007.4424456"},{"key":"12_CR11","first-page":"553","volume":"18","author":"A.W.F. Edwards","year":"1963","unstructured":"Edwards, A.W.F., Cavalli-Sforza, L.L.: The reconstruction of evolution. Heredity\u00a018, 553 (1963)","journal-title":"Heredity"},{"issue":"6","key":"12_CR12","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1007\/BF01734359","volume":"17","author":"J. Felsenstein","year":"1981","unstructured":"Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution\u00a017(6), 368\u2013376 (1981)","journal-title":"Journal of Molecular Evolution"},{"issue":"1","key":"12_CR13","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/BF00487738","volume":"1","author":"W.M. Fitch","year":"1967","unstructured":"Fitch, W.M., Margoliash, E.: A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case. Biochemical Genetics\u00a01(1), 65\u201371 (1967)","journal-title":"Biochemical Genetics"},{"issue":"4","key":"12_CR14","doi-asserted-by":"publisher","first-page":"826","DOI":"10.1137\/0132071","volume":"32","author":"M.R. Garey","year":"1977","unstructured":"Garey, M.R., Johnson, D.S.: The rectilinear Steiner tree problem is NP-Complete. SIAM Journal on Applied Mathematics\u00a032(4), 826\u2013834 (1977)","journal-title":"SIAM Journal on Applied Mathematics"},{"key":"12_CR15","unstructured":"Go\u00ebffon, A.: Nouvelles heuristiques de voisinage et m\u00e9m\u00e9tiques pour le probl\u00e8me maximum de parcimonie. Ph.D. thesis, LERIA, Universit\u00e9 d\u2019Angers (2006)"},{"key":"12_CR16","doi-asserted-by":"crossref","unstructured":"Gunawan, A., Lau, H.C., Lindawati: Fine-tuning algorithm parameters using the design of experiments. LNCS, vol.\u00a06683, pp. 131\u2013145 (2011)","DOI":"10.1007\/978-3-642-25566-3_21"},{"key":"12_CR17","doi-asserted-by":"crossref","unstructured":"Gusfield, D.: Algorithms on strings, trees, and sequences: Computer science and computational biology, 1st edn. Cambridge University Press (1997)","DOI":"10.1017\/CBO9780511574931"},{"issue":"2","key":"12_CR18","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1016\/0025-5564(82)90027-X","volume":"59","author":"M.D. Hendy","year":"1982","unstructured":"Hendy, M.D., Penny, D.: Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences\u00a059(2), 277\u2013290 (1982)","journal-title":"Mathematical Biosciences"},{"key":"12_CR19","volume-title":"Phylogeny","author":"W. Hennig","year":"1966","unstructured":"Hennig, W.: Phylogenetic systematics. Phylogeny. University of Illinois Press, Urbana (1966)"},{"key":"12_CR20","volume-title":"Molecular systematics","author":"D.M. Hillis","year":"1996","unstructured":"Hillis, D.M., Moritz, C., Mable, B.K.: Molecular systematics, 2nd edn. Sinauer Associates Inc., Sunderland (1996)","edition":"2"},{"issue":"6","key":"12_CR21","doi-asserted-by":"publisher","first-page":"865","DOI":"10.1287\/opre.37.6.865","volume":"37","author":"D.S. Johnson","year":"1989","unstructured":"Johnson, D.S., Aragon, C.R., McGeoch, L.A., Schevon, C.: Optimization by simulated annealing: An experimental evaluation; part I, graph partitioning. Operations Research\u00a037(6), 865\u2013892 (1989)","journal-title":"Operations Research"},{"issue":"3","key":"12_CR22","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1287\/opre.39.3.378","volume":"39","author":"D.S. Johnson","year":"1991","unstructured":"Johnson, D.S., Aragon, C.R., McGeoch, L.A., Schevon, C.: Optimization by simulated annealing: An experimental evaluation; part II, graph coloring and number partitioning. Operations Research\u00a039(3), 378\u2013406 (1991)","journal-title":"Operations Research"},{"key":"12_CR23","doi-asserted-by":"crossref","unstructured":"L\u00fc, Z., Hao, J.K., Glover, F.: Neighborhood analysis: A case study on curriculum-based course timetabling. Journal of Heuristics\u00a017(2) (2011)","DOI":"10.1007\/s10732-010-9128-0"},{"key":"12_CR24","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/297197a0","volume":"297","author":"D. Penny","year":"1982","unstructured":"Penny, D., Foulds, L.R., Hendy, M.D.: Testing the theory of evolution by comparing phylogenetic trees constructed from five different protein sequences. Nature\u00a0297, 197\u2013200 (1982)","journal-title":"Nature"},{"key":"12_CR25","unstructured":"Ribeiro, C.C., Vianna, D.S.: A genetic algorithm for the phylogeny problem using an optimized crossover strategy based on path-relinking. In: Proceedings of the II Workshop Brasileiro de Bioinform\u00e1tica, Maca\u00e9, Brazil, pp. 97\u2013102 (2003)"},{"issue":"3","key":"12_CR26","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1111\/j.1475-3995.2005.498_1.x","volume":"12","author":"C.C. Ribeiro","year":"2005","unstructured":"Ribeiro, C.C., Vianna, D.S.: A GRASP\/VND heuristic for the phylogeny problem using a new neighborhood structure. International Transactions in Operational Research\u00a012(3), 325\u2013338 (2005)","journal-title":"International Transactions in Operational Research"},{"issue":"5","key":"12_CR27","doi-asserted-by":"publisher","first-page":"641","DOI":"10.1111\/j.1475-3995.2009.00699.x","volume":"16","author":"C.C. Ribeiro","year":"2009","unstructured":"Ribeiro, C.C., Vianna, D.S.: A hybrid genetic algorithm for the phylogeny problem using path-relinking as a progressive crossover strategy. International Transactions in Operational Research\u00a016(5), 641\u2013657 (2009)","journal-title":"International Transactions in Operational Research"},{"key":"12_CR28","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1007\/978-3-642-01184-9_15","volume-title":"Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics","author":"J.-M. Richer","year":"2009","unstructured":"Richer, J.-M., Go\u00ebffon, A., Hao, J.-K.: A Memetic Algorithm for Phylogenetic Reconstruction with Maximum Parsimony. In: Pizzuti, C., Ritchie, M.D., Giacobini, M. (eds.) EvoBIO 2009. LNCS, vol.\u00a05483, pp. 164\u2013175. Springer, Heidelberg (2009)"},{"issue":"2","key":"12_CR29","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/0095-8956(71)90020-7","volume":"11","author":"D.F. Robinson","year":"1971","unstructured":"Robinson, D.F.: Comparison of labeled trees with valency three. Journal of Combinatorial Theory, Series B\u00a011(2), 105\u2013119 (1971)","journal-title":"Journal of Combinatorial Theory, Series B"},{"issue":"10","key":"12_CR30","doi-asserted-by":"publisher","first-page":"3331","DOI":"10.1016\/j.cor.2007.03.001","volume":"35","author":"E. Rodriguez-Tello","year":"2008","unstructured":"Rodriguez-Tello, E., Hao, J.K., Torres-Jimenez, J.: An effective two-stage simulated annealing algorithm for the minimum linear arrangement problem. Computers & Operations Research\u00a035(10), 3331\u20133346 (2008)","journal-title":"Computers & Operations Research"},{"key":"12_CR31","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1007\/978-3-642-14156-0_8","volume-title":"Artifical Evolution","author":"E. Rodriguez-Tello","year":"2010","unstructured":"Rodriguez-Tello, E., Torres-Jimenez, J.: Memetic Algorithms for Constructing Binary Covering Arrays of Strength Three. In: Collet, P., Monmarch\u00e9, N., Legrand, P., Schoenauer, M., Lutton, E. (eds.) EA 2009. LNCS, vol.\u00a05975, pp. 86\u201397. Springer, Heidelberg (2010)"},{"issue":"4","key":"12_CR32","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\u00a04(4), 406\u2013425 (1987)","journal-title":"Molecular Biology and Evolution"},{"key":"12_CR33","doi-asserted-by":"crossref","unstructured":"Skourikhine, A.: Phylogenetic tree reconstruction using self-adaptive genetic algorithm. In: Proceedings of the IEEE International Symposium on Bio-Informatics and Biomedical Engineering, Arlington, VA, USA, pp. 129\u2013134 (2000)","DOI":"10.1109\/BIBE.2000.889599"},{"key":"12_CR34","doi-asserted-by":"crossref","unstructured":"Sober, E.: The nature of selection: Evolutionary theory in philosophical focus. University Of Chicago Press (1993)","DOI":"10.7208\/chicago\/9780226308883.001.0001"},{"key":"12_CR35","doi-asserted-by":"crossref","unstructured":"Sridhar, S., Lam, F., Blelloch, G.E., Ravi, R., Schwartz, R.: Direct maximum parsimony phylogeny reconstruction from genotype data. BMC Bioinformatics\u00a08(472) (2007)","DOI":"10.1186\/1471-2105-8-472"},{"key":"12_CR36","first-page":"411","volume-title":"Molecular Systematics","author":"D.L. Swofford","year":"1996","unstructured":"Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M.: Phylogeny reconstruction. In: Molecular Systematics, 2nd edn., ch.\u00a011, pp. 411\u2013501. Sinauer Associates, Inc., Sunderland (1996)","edition":"2"},{"key":"12_CR37","doi-asserted-by":"crossref","unstructured":"Van Laarhoven, P.J.M., Aarts, E.H.L.: Simulated annealing: Theory and applications. Kluwer Academic Publishers (1988)","DOI":"10.1007\/978-94-015-7744-1"},{"key":"12_CR38","unstructured":"Vazquez-Ortiz, K.E.: Metaheur\u00edsticas para la resoluci\u00f3n del problema de m\u00e1xima parsimonia. Master\u2019s thesis, LTI, Cinvestav - Tamaulipas, Cd. Vitoria, Tamps. Mexico (2011)"},{"issue":"4","key":"12_CR39","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1016\/0022-5193(78)90137-6","volume":"73","author":"M.S. Waterman","year":"1978","unstructured":"Waterman, M.S., Smith, T.F.: On the similarity of dendrograms. Journal of Theoretical Biology\u00a073(4), 784\u2013800 (1978)","journal-title":"Journal of Theoretical Biology"},{"key":"12_CR40","doi-asserted-by":"crossref","unstructured":"Xiong, J.: Essential Bioinformatics, 1st edn. Cambridge University Press (2006)","DOI":"10.1017\/CBO9780511806087"}],"container-title":["Advances in Intelligent Systems and Computing","EVOLVE - A Bridge between Probability, Set Oriented Numerics, and Evolutionary Computation II"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-31519-0_12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,6]],"date-time":"2025-04-06T21:06:13Z","timestamp":1743973573000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-642-31519-0_12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013]]},"ISBN":["9783642315183","9783642315190"],"references-count":40,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-31519-0_12","relation":{},"ISSN":["2194-5357","2194-5365"],"issn-type":[{"type":"print","value":"2194-5357"},{"type":"electronic","value":"2194-5365"}],"subject":[],"published":{"date-parts":[[2013]]}}}