{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T10:30:39Z","timestamp":1760783439376,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":43,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642230370"},{"type":"electronic","value":"9783642230387"}],"license":[{"start":{"date-parts":[[2011,1,1]],"date-time":"2011-01-01T00:00:00Z","timestamp":1293840000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011]]},"DOI":"10.1007\/978-3-642-23038-7_16","type":"book-chapter","created":{"date-parts":[[2011,8,30]],"date-time":"2011-08-30T13:06:43Z","timestamp":1314709603000},"page":"175-187","source":"Crossref","is-referenced-by-count":2,"title":["Bootstrapping Phylogenies Inferred from Rearrangement Data"],"prefix":"10.1007","author":[{"given":"Yu","family":"Lin","sequence":"first","affiliation":[]},{"given":"Vaibhav","family":"Rajan","sequence":"additional","affiliation":[]},{"given":"Bernard M. E.","family":"Moret","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"issue":"2","key":"16_CR1","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/S1055-7903(03)00118-0","volume":"28","author":"H. Amrine-Madsen","year":"2003","unstructured":"Amrine-Madsen, H., Koepfli, K.P., Wayne, R., Springer, M.: A new phylogenetic marker, apolipoprotein b, provides compelling evidence for eutherian relationships. Mol. Phyl. Evol.\u00a028(2), 225\u2013240 (2003)","journal-title":"Mol. Phyl. Evol."},{"issue":"4","key":"16_CR2","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1080\/10635150600755453","volume":"55","author":"M. Anisimova","year":"2006","unstructured":"Anisimova, M., Gascuel, O.: Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol.\u00a055(4), 539\u2013552 (2006)","journal-title":"Syst. Biol."},{"key":"16_CR3","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"163","DOI":"10.1007\/11851561_16","volume-title":"Algorithms in Bioinformatics","author":"A. Bergeron","year":"2006","unstructured":"Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: B\u00fccher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol.\u00a04175, pp. 163\u2013173. Springer, Heidelberg (2006)"},{"key":"16_CR4","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1371\/journal.pcbi.0030002","volume":"3","author":"G. Cannarozzi","year":"2007","unstructured":"Cannarozzi, G., Schneider, A., Gonnet, G.: A phylogenomic study of human, dog, and mouse. PLoS Comput. Biol.\u00a03, e2 (2007)","journal-title":"PLoS Comput. Biol."},{"issue":"3","key":"16_CR5","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1093\/molbev\/msh049","volume":"21","author":"R. Desper","year":"2003","unstructured":"Desper, R., Gascuel, O.: Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol.\u00a021(3), 587\u2013598 (2003)","journal-title":"Mol. Biol. Evol."},{"issue":"1","key":"16_CR6","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1080\/00031305.1983.10483087","volume":"37","author":"B. Efron","year":"1983","unstructured":"Efron, B., Gong, G.: A leisurely look at the bootstrap, the jackknife, and cross-validation. American Statistician\u00a037(1), 36\u201348 (1983)","journal-title":"American Statistician"},{"key":"16_CR7","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4899-4541-9","volume-title":"An Introduction to the Bootstrap","author":"B. Efron","year":"1993","unstructured":"Efron, B., Tibshirani, R., Tibshirani, R.: An Introduction to the Bootstrap. Chapman & Hall\/CRC, Boca Raton (1993)"},{"issue":"4","key":"16_CR8","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1111\/j.1463-6409.1997.tb00420.x","volume":"26","author":"J. Farris","year":"1997","unstructured":"Farris, J.: The future of phylogeny reconstruction. Zoologica Scripta\u00a026(4), 303\u2013311 (1997)","journal-title":"Zoologica Scripta"},{"issue":"2","key":"16_CR9","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1111\/j.1096-0031.1996.tb00196.x","volume":"12","author":"J. Farris","year":"1996","unstructured":"Farris, J., Albert, V., K\u00e4llersj\u00f6, M., Lipscomb, D., Kluge, A.: Parsimony jackknifing outperforms neighbor-joining. Cladistics\u00a012(2), 99\u2013124 (1996)","journal-title":"Cladistics"},{"key":"16_CR10","doi-asserted-by":"publisher","first-page":"783","DOI":"10.2307\/2408678","volume":"39","author":"J. Felsenstein","year":"1985","unstructured":"Felsenstein, J.: Confidence limits on phylogenies: an approach using the bootstrap. Evol.\u00a039, 783\u2013791 (1985)","journal-title":"Evol."},{"issue":"2","key":"16_CR11","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1093\/sysbio\/42.2.193","volume":"42","author":"J. Felsenstein","year":"1993","unstructured":"Felsenstein, J., Kishino, H.: Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol.\u00a042(2), 193\u2013200 (1993)","journal-title":"Syst. Biol."},{"key":"16_CR12","doi-asserted-by":"publisher","DOI":"10.7551\/mitpress\/9780262062824.001.0001","volume-title":"Combinatorics of Genome Rearrangements","author":"G. Fertin","year":"2009","unstructured":"Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. MIT Press, Cambridge (2009)"},{"issue":"5","key":"16_CR13","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1080\/10635150390235520","volume":"52","author":"S. Guindon","year":"2003","unstructured":"Guindon, S., Gascuel, O.: PHYML\u2014a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol.\u00a052(5), 696\u2013704 (2003)","journal-title":"Syst. Biol."},{"key":"16_CR14","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1126\/science.267.5195.255","volume":"267","author":"D. Hillis","year":"1995","unstructured":"Hillis, D., Huelsenbeck, J.: Assessing molecular phylogenies. Science\u00a0267, 255\u2013256 (1995)","journal-title":"Science"},{"issue":"2","key":"16_CR15","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1214\/ss\/1063994979","volume":"18","author":"S. Holmes","year":"2003","unstructured":"Holmes, S.: Bootstrapping phylogenetic trees: theory and methods. Statistical Science\u00a018(2), 241\u2013255 (2003)","journal-title":"Statistical Science"},{"key":"16_CR16","volume-title":"Proc. 8th IEEE Symp. Comput. Intell. in Bioinf. & Comput. Biol. (CIBCB 2011)","author":"F. Hu","year":"2011","unstructured":"Hu, F., Gao, N., Tang, J.: Maximum likelihood phylogenetic reconstruction using gene order encodings. In: Proc. 8th IEEE Symp. Comput. Intell. in Bioinf. & Comput. Biol. (CIBCB 2011). IEEE Press, Los Alamitos (accepted, to appear 2011)"},{"issue":"8","key":"16_CR17","doi-asserted-by":"publisher","first-page":"1722","DOI":"10.1093\/molbev\/msm094","volume":"24","author":"G. Huttley","year":"2007","unstructured":"Huttley, G., Wakefield, M., Easteal, S.: Rates of genome evolution and branching order from whole-genome analysis. Mol. Biol. Evol.\u00a024(8), 1722\u20131730 (2007)","journal-title":"Mol. Biol. Evol."},{"key":"#cr-split#-16_CR18.1","doi-asserted-by":"crossref","unstructured":"Lin, Y., Moret, B.: Estimating true evolutionary distances under the DCJ model. In: Proc. 16th Int'l Conf. on Intelligent Systems for Mol. Biol. (ISMB 2008) (2008)","DOI":"10.1093\/bioinformatics\/btn148"},{"key":"#cr-split#-16_CR18.2","doi-asserted-by":"crossref","unstructured":"Bioinformatics 24(13), i114-i122 (2008)","DOI":"10.1093\/bioinformatics\/btn148"},{"key":"16_CR19","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1007\/978-3-642-16181-0_12","volume-title":"Comparative Genomics","author":"Y. Lin","year":"2010","unstructured":"Lin, Y., Rajan, V., Moret, B.: Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol.\u00a06398, pp. 137\u2013148. Springer, Heidelberg (2010)"},{"key":"#cr-split#-16_CR20.1","doi-asserted-by":"crossref","unstructured":"Lin, Y., Rajan, V., Swenson, K., Moret, B.: Estimating true evolutionary distances under rearrangements, duplications, and losses. In: Proc. 8th Asia Pacific Bioinf. Conf. (APBC 2010) (2010)","DOI":"10.1186\/1471-2105-11-S1-S54"},{"key":"#cr-split#-16_CR20.2","doi-asserted-by":"crossref","unstructured":"BMC Bioinformatics 11(suppl. 1), s54 (2010)","DOI":"10.1186\/1471-2164-11-S4-S1"},{"key":"16_CR21","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1038\/35054544","volume":"409","author":"O. Madsen","year":"2001","unstructured":"Madsen, O., et al.: Parallel adaptive radiations in two major clades of placental mammals. Nature\u00a0409, 610\u2013614 (2001)","journal-title":"Nature"},{"issue":"3","key":"16_CR22","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1016\/j.tcs.2004.02.039","volume":"325","author":"M. Marron","year":"2004","unstructured":"Marron, M., Swenson, K., Moret, B.: Genomic distances under deletions and insertions. Theor. Comput. Sci.\u00a0325(3), 347\u2013360 (2004)","journal-title":"Theor. Comput. Sci."},{"issue":"3","key":"16_CR23","doi-asserted-by":"publisher","first-page":"508","DOI":"10.1016\/S0022-0000(02)00007-7","volume":"65","author":"B. Moret","year":"2002","unstructured":"Moret, B., Tang, J., Wang, L.S., Warnow, T.: Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci.\u00a065(3), 508\u2013525 (2002)","journal-title":"J. Comput. Syst. Sci."},{"key":"16_CR24","series-title":"Methods in Enzymology","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1016\/S0076-6879(05)95035-0","volume-title":"Molecular Evolution: Producing the Biochemical Data, Part B","author":"B. Moret","year":"2005","unstructured":"Moret, B., Warnow, T.: Advances in phylogeny reconstruction from gene order and content data. In: Zimmer, E., Roalson, E. (eds.) Molecular Evolution: Producing the Biochemical Data, Part B. Methods in Enzymology, vol.\u00a0395, pp. 673\u2013700. Elsevier, Amsterdam (2005)"},{"issue":"1","key":"16_CR25","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1080\/10635150050207456","volume":"49","author":"M. Mort","year":"2000","unstructured":"Mort, M., Soltis, P., Soltis, D., Mabry, M.: Comparison of three methods for estimating internal support on phylogenetic trees. Syst. Biol.\u00a049(1), 160\u2013171 (2000)","journal-title":"Syst. Biol."},{"key":"16_CR26","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1038\/35054550","volume":"409","author":"W. Murphy","year":"2001","unstructured":"Murphy, W., Eizirik, E., Johnson, W., Zhang, Y., Ryder, O., O\u2019Brien, S.: Molecular phylogenetics and the origins of placental mammals. Nature\u00a0409, 614\u2013618 (2001)","journal-title":"Nature"},{"key":"16_CR27","unstructured":"R Development Core Team: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing (2009)"},{"key":"16_CR28","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1016\/S0169-5347(00)01967-4","volume":"15","author":"A. Rokas","year":"2000","unstructured":"Rokas, A., Holland, P.: Rare genomic changes as a tool for phylogenetics. Trends in Ecol. and Evol.\u00a015, 454\u2013459 (2000)","journal-title":"Trends in Ecol. and Evol."},{"key":"16_CR29","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. Mol. Biol. Evol.\u00a04, 406\u2013425 (1987)","journal-title":"Mol. Biol. Evol."},{"issue":"3","key":"16_CR30","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1016\/S1055-7903(03)00011-3","volume":"27","author":"N. Salamin","year":"2003","unstructured":"Salamin, N., Chase, M., Hodkinson, T., Savolainen, V.: Assessing internal support with large phylogenetic DNA matrices. Mol. Phyl. Evol.\u00a027(3), 528 (2003)","journal-title":"Mol. Phyl. Evol."},{"issue":"3","key":"16_CR31","doi-asserted-by":"publisher","first-page":"1176","DOI":"10.1214\/aos\/1176347263","volume":"17","author":"J. Shao","year":"1989","unstructured":"Shao, J., Wu, C.: A general theory for jackknife variance estimation. Annals of Statistics\u00a017(3), 1176\u20131197 (1989)","journal-title":"Annals of Statistics"},{"issue":"1","key":"16_CR32","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/1471-2105-11-168","volume":"11","author":"J. Shi","year":"2010","unstructured":"Shi, J., Zhang, Y., Luo, H., Tang, J.: Using jackknife to assess the quality of gene order phylogenies. BMC Bioinformatics\u00a011(1), 168 (2010)","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"16_CR33","doi-asserted-by":"publisher","first-page":"256","DOI":"10.1214\/ss\/1063994980","volume":"18","author":"P. Soltis","year":"2003","unstructured":"Soltis, P., Soltis, D.: Applying the bootstrap in phylogeny reconstruction. Statist. Sci.\u00a018(2), 256\u2013267 (2003)","journal-title":"Statist. Sci."},{"key":"16_CR34","volume-title":"Proc. 7th SIAM Workshop on Algorithm Engineering & Experiments (ALENEX 2005)","author":"K. Swenson","year":"2005","unstructured":"Swenson, K., Marron, M., Earnest-DeYoung, J., Moret, B.: Approximating the true evolutionary distance between two genomes. In: Proc. 7th SIAM Workshop on Algorithm Engineering & Experiments (ALENEX 2005). SIAM Press, Philadelphia (2005)"},{"key":"16_CR35","unstructured":"Swofford, D., Olson, G., Waddell, P., Hillis, D.: Phylogenetic inference. In: Hillis, D., Moritz, C., Mable, B. (eds.) Molecular Systematics, 2nd edn., ch.\u00a011. Sinauer Assoc. (1996)"},{"key":"16_CR36","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-642-04744-2_1","volume-title":"Comparative Genomics","author":"E. Tannier","year":"2009","unstructured":"Tannier, E.: Yeast ancestral genome reconstructions: The possibilities of computational methods. In: Ciccarelli, F.D., Mikl\u00f3s, I. (eds.) RECOMB-CG 2009. LNCS, vol.\u00a05817, pp. 1\u201312. Springer, Heidelberg (2009)"},{"key":"16_CR37","first-page":"637","volume-title":"Proc. 33rd Ann. ACM Symp. Theory of Comput. (STOC 2001)","author":"L.S. Wang","year":"2001","unstructured":"Wang, L.S.: Exact-IEBP: a new technique for estimating evolutionary distances between whole genomes. In: Proc. 33rd Ann. ACM Symp. Theory of Comput. (STOC 2001), pp. 637\u2013646. ACM Press, New York (2001)"},{"key":"16_CR38","first-page":"524","volume-title":"Proc. 7th Pacific Symp. on Biocomputing (PSB 2002)","author":"L.S. Wang","year":"2002","unstructured":"Wang, L.S., Jansen, R., Moret, B., Raubeson, L., Warnow, T.: Fast phylogenetic methods for genome rearrangement evolution: An empirical study. In: Proc. 7th Pacific Symp. on Biocomputing (PSB 2002), pp. 524\u2013535. World Scientific Pub., Singapore (2002)"},{"key":"16_CR39","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1007\/3-540-44696-6_14","volume-title":"Algorithms in Bioinformatics","author":"L.S. Wang","year":"2001","unstructured":"Wang, L.S., Warnow, T.: Estimating true evolutionary distances between genomes. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol.\u00a02149, pp. 176\u2013190. Springer, Heidelberg (2001)"},{"issue":"36","key":"16_CR40","doi-asserted-by":"publisher","first-page":"14395","DOI":"10.1073\/pnas.0704342104","volume":"104","author":"D. Wildman","year":"2007","unstructured":"Wildman, D., et al.: Genomics, biogeography, and the diversification of placental mammals. Proc. Nat\u2019l. Acad. Sci., USA\u00a0104(36), 14395\u201314400 (2007)","journal-title":"Proc. Nat\u2019l. Acad. Sci., USA"},{"issue":"16","key":"16_CR41","doi-asserted-by":"publisher","first-page":"3340","DOI":"10.1093\/bioinformatics\/bti535","volume":"21","author":"S. Yancopoulos","year":"2005","unstructured":"Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics\u00a021(16), 3340\u20133346 (2005)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Algorithms in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-23038-7_16","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T18:29:33Z","timestamp":1712773773000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-23038-7_16"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011]]},"ISBN":["9783642230370","9783642230387"],"references-count":43,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-23038-7_16","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2011]]}}}