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Volumn 7, Issue 1, 2012, Pages

Bootstrapping phylogenies inferred from rearrangement data

Author keywords

Bootstrap; Comparative genomics; Gene order; Jackknife; Phylogenetic reconstruction; Rearrangement

Indexed keywords

MAMMALIA;

EID: 84865433550     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-7-21     Document Type: Article
Times cited : (12)

References (48)
  • 5
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: an approach using the bootstrap
    • Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evol 1985, 39:783-791.
    • (1985) Evol , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 6
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative
    • 10.1080/10635150600755453, 16785212
    • Anisimova M, Gascuel O. Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 2006, 55(4):539-552. 10.1080/10635150600755453, 16785212.
    • (2006) Syst Biol , vol.55 , Issue.4 , pp. 539-552
    • Anisimova, M.1    Gascuel, O.2
  • 7
    • 0242578620 scopus 로고    scopus 로고
    • PHYML-A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • 10.1080/10635150390235520, 14530136
    • Guindon S, Gascuel O. PHYML-A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520, 14530136.
    • (2003) Syst Biol , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 8
    • 77950533243 scopus 로고    scopus 로고
    • Using jackknife to assess the quality of gene order phylogenies
    • 10.1186/1471-2105-11-168, 2858039, 20370914
    • Shi J, Zhang Y, Luo H, Tang J. Using jackknife to assess the quality of gene order phylogenies. BMC Bioinformatics 2010, 11:168. 10.1186/1471-2105-11-168, 2858039, 20370914.
    • (2010) BMC Bioinformatics , vol.11 , pp. 168
    • Shi, J.1    Zhang, Y.2    Luo, H.3    Tang, J.4
  • 10
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 11
    • 1542510099 scopus 로고    scopus 로고
    • Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting
    • 10.1093/molbev/msh049, 14694080
    • 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 2003, 21(3):587-598. 10.1093/molbev/msh049, 14694080.
    • (2003) Mol Biol Evol , vol.21 , Issue.3 , pp. 587-598
    • Desper, R.1    Gascuel, O.2
  • 12
    • 4544242008 scopus 로고    scopus 로고
    • Genomic distances under deletions and insertions
    • Marron M, Swenson K, Moret B. Genomic distances under deletions and insertions. Theor Comput Sci 2004, 325(3):347-360.
    • (2004) Theor Comput Sci , vol.325 , Issue.3 , pp. 347-360
    • Marron, M.1    Swenson, K.2    Moret, B.3
  • 16
    • 0346925690 scopus 로고
    • Approximate tests of correlation in time-series 3
    • Quenouille M. Approximate tests of correlation in time-series 3. Math Proc Cambridge Philos Soc 1949, 45(3):483-484.
    • (1949) Math Proc Cambridge Philos Soc , vol.45 , Issue.3 , pp. 483-484
    • Quenouille, M.1
  • 17
    • 0001617782 scopus 로고
    • Bias and confidence in not quite large samples
    • Tukey J. Bias and confidence in not quite large samples. Ann Math Stat 1958, 29(2):614.
    • (1958) Ann Math Stat , vol.29 , Issue.2 , pp. 614
    • Tukey, J.1
  • 18
    • 0002344794 scopus 로고
    • Bootstrap methods: another look at the jackknife
    • Efron B. Bootstrap methods: another look at the jackknife. Ann Stat 1979, 7:1-26.
    • (1979) Ann Stat , vol.7 , pp. 1-26
    • Efron, B.1
  • 19
    • 84868575783 scopus 로고
    • The jackknife, the bootstrap and other resampling plans
    • SIAM, Efron B
    • Efron B The jackknife, the bootstrap and other resampling plans. CBMS-NSF Regional Conf Series in Applied Math, Volume 38 1982, SIAM, Efron B.
    • (1982) CBMS-NSF Regional Conf Series in Applied Math, Volume 38
  • 20
    • 84945737762 scopus 로고
    • A leisurely look at the bootstrap, the jackknife, and cross-validation
    • Efron B, Gong G. A leisurely look at the bootstrap, the jackknife, and cross-validation. Am Statistician 1983, 37:36-48.
    • (1983) Am Statistician , vol.37 , pp. 36-48
    • Efron, B.1    Gong, G.2
  • 21
    • 0015971972 scopus 로고
    • The jackknife-a review
    • Miller R. The jackknife-a review. Biometrika 1974, 61:1.
    • (1974) Biometrika , vol.61 , pp. 1
    • Miller, R.1
  • 22
    • 0001077032 scopus 로고
    • Nonparametric estimates of standard error: the jackknife, the bootstrap and other methods
    • Efron B. Nonparametric estimates of standard error: the jackknife, the bootstrap and other methods. Biometrika 1981, 68(3):589.
    • (1981) Biometrika , vol.68 , Issue.3 , pp. 589
    • Efron, B.1
  • 23
    • 0347532847 scopus 로고    scopus 로고
    • Applying the bootstrap in phylogeny reconstruction
    • Soltis P, Soltis D. Applying the bootstrap in phylogeny reconstruction. Statist Sci 2003, 18(2):256-267.
    • (2003) Statist Sci , vol.18 , Issue.2 , pp. 256-267
    • Soltis, P.1    Soltis, D.2
  • 24
    • 0346271739 scopus 로고    scopus 로고
    • Bootstrapping phylogenetic trees: theory and methods
    • Holmes S. Bootstrapping phylogenetic trees: theory and methods. Stat Sci 2003, 18(2):241-255.
    • (2003) Stat Sci , vol.18 , Issue.2 , pp. 241-255
    • Holmes, S.1
  • 25
    • 12044259827 scopus 로고
    • Is There Something Wrong with the Bootstrap on Phylogenies? A Reply to Hillis and Bull
    • Felsenstein J, Kishino H. Is There Something Wrong with the Bootstrap on Phylogenies? A Reply to Hillis and Bull. Syst Biol 1993, 42(2):193-200.
    • (1993) Syst Biol , vol.42 , Issue.2 , pp. 193-200
    • Felsenstein, J.1    Kishino, H.2
  • 26
    • 0001514453 scopus 로고
    • A general theory for jackknife variance estimation
    • Shao J, Wu C. A general theory for jackknife variance estimation. Ann Stat 1989, 17(3):1176-1197.
    • (1989) Ann Stat , vol.17 , Issue.3 , pp. 1176-1197
    • Shao, J.1    Wu, C.2
  • 27
    • 0031421547 scopus 로고    scopus 로고
    • The future of phylogeny reconstruction
    • Farris J. The future of phylogeny reconstruction. Zoologica Scr 1997, 26(4):303-311.
    • (1997) Zoologica Scr , vol.26 , Issue.4 , pp. 303-311
    • Farris, J.1
  • 29
    • 0038781911 scopus 로고    scopus 로고
    • Assessing internal support with large phylogenetic DNA matrices
    • Salamin N, Chase M, Hodkinson T, Savolainen V. Assessing internal support with large phylogenetic DNA matrices. Mol Phyl Evol 2003, 27(3):528.
    • (2003) Mol Phyl Evol , vol.27 , Issue.3 , pp. 528
    • Salamin, N.1    Chase, M.2    Hodkinson, T.3    Savolainen, V.4
  • 30
    • 0034350373 scopus 로고    scopus 로고
    • Comparison of three methods for estimating internal support on phylogenetic trees
    • 10.1080/10635150050207456, 12116478
    • Mort M, Soltis P, Soltis D, Mabry M. Comparison of three methods for estimating internal support on phylogenetic trees. Syst Biol 2000, 49:160-171. 10.1080/10635150050207456, 12116478.
    • (2000) Syst Biol , vol.49 , pp. 160-171
    • Mort, M.1    Soltis, P.2    Soltis, D.3    Mabry, M.4
  • 31
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • Rokas A, Holland P. Rare genomic changes as a tool for phylogenetics. Trends in Ecol and Evol 2000, 15:454-459.
    • (2000) Trends in Ecol and Evol , vol.15 , pp. 454-459
    • Rokas, A.1    Holland, P.2
  • 32
    • 0003689342 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Sunderland, Sinauer Assoc, Hillis D, Moritz C, Mable B
    • Swofford D, Olson G, Waddell P, Hillis D. Phylogenetic inference. 2nd ed 1996, Sunderland, Sinauer Assoc, Hillis D, Moritz C, Mable B.
    • (1996) 2nd ed
    • Swofford, D.1    Olson, G.2    Waddell, P.3    Hillis, D.4
  • 33
    • 23844520968 scopus 로고    scopus 로고
    • Steps toward accurate reconstructions of phylogenies from gene-order data
    • Moret B, Tang J, Wang LS, Warnow T. Steps toward accurate reconstructions of phylogenies from gene-order data. J Comput Syst Sci 2002, 65(3):508-525.
    • (2002) J Comput Syst Sci , vol.65 , Issue.3 , pp. 508-525
    • Moret, B.1    Tang, J.2    Wang, L.S.3    Warnow, T.4
  • 34
    • 84961146708 scopus 로고    scopus 로고
    • Exact-IEBP: a new technique for estimating evolutionary distances between whole genomes
    • ACM Press, New York
    • Wang LS. Exact-IEBP: a new technique for estimating evolutionary distances between whole genomes. Proc 33rd Ann ACM Symp Theory of Comput (STOC'01) 2001, 637-646. ACM Press, New York.
    • (2001) Proc 33rd Ann ACM Symp Theory of Comput (STOC'01) , pp. 637-646
    • Wang, L.S.1
  • 36
    • 2642613543 scopus 로고
    • Assessing molecular phylogenies
    • 10.1126/science.267.5195.255, 17791347
    • Hillis D, Huelsenbeck J. Assessing molecular phylogenies. Science 1995, 267:255-256. 10.1126/science.267.5195.255, 17791347.
    • (1995) Science , vol.267 , pp. 255-256
    • Hillis, D.1    Huelsenbeck, J.2
  • 38
    • 24044535485 scopus 로고    scopus 로고
    • Efficient sorting of genomic permutations by translocation, inversion and block interchange
    • 10.1093/bioinformatics/bti535, 15951307
    • Yancopoulos S, Attie O, Friedberg R. Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 2005, 21(16):3340-3346. 10.1093/bioinformatics/bti535, 15951307.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3340-3346
    • Yancopoulos, S.1    Attie, O.2    Friedberg, R.3
  • 41
    • 0035252080 scopus 로고    scopus 로고
    • Molecular phylogenetics and the origins of placental mammals
    • 10.1038/35054550, 11214319
    • Murphy W, Eizirik E, Johnson W, Zhang Y, Ryder O, O'Brien S. Molecular phylogenetics and the origins of placental mammals. Nature 2001, 409:614-618. 10.1038/35054550, 11214319.
    • (2001) Nature , vol.409 , pp. 614-618
    • Murphy, W.1    Eizirik, E.2    Johnson, W.3    Zhang, Y.4    Ryder, O.5    O'Brien, S.6
  • 42
    • 0141609704 scopus 로고    scopus 로고
    • A new phylogenetic marker, apolipoprotein B , provides compelling evidence for eutherian relationships
    • Amrine-Madsen H, Koepfli KP, Wayne R, Springer M. A new phylogenetic marker, apolipoprotein B , provides compelling evidence for eutherian relationships. Mol Phyl Evol 2003, 28(2):225-240.
    • (2003) Mol Phyl Evol , vol.28 , Issue.2 , pp. 225-240
    • Amrine-Madsen, H.1    Koepfli, K.P.2    Wayne, R.3    Springer, M.4
  • 43
    • 34547753508 scopus 로고    scopus 로고
    • Rates of genome evolution and branching order from whole-genome analysis
    • 10.1093/molbev/msm094, 17494028
    • Huttley G, Wakefield M, Easteal S. Rates of genome evolution and branching order from whole-genome analysis. Mol Biol Evol 2007, 24(8):1722-1730. 10.1093/molbev/msm094, 17494028.
    • (2007) Mol Biol Evol , vol.24 , Issue.8 , pp. 1722-1730
    • Huttley, G.1    Wakefield, M.2    Easteal, S.3
  • 45
    • 33846491679 scopus 로고    scopus 로고
    • A phylogenomic study of human, dog, and mouse
    • 10.1371/journal.pcbi.0030002, 1761043, 17206860
    • Cannarozzi G, Schneider A, Gonnet G. A phylogenomic study of human, dog, and mouse. PLoS Comput Biol 2007, 3:e2. 10.1371/journal.pcbi.0030002, 1761043, 17206860.
    • (2007) PLoS Comput Biol , vol.3
    • Cannarozzi, G.1    Schneider, A.2    Gonnet, G.3


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