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Volumn 19, Issue 12, 2002, Pages 2051-2059

δ plots: A tool for analyzing phylogenetic distance data

Author keywords

Assessment of data quality; Genetic distance; Phylogenetic analysis; Recombination; Statistical geometry; Tree reconstruction

Indexed keywords

ARTICLE; CANDIDA ALBICANS; DATA ANALYSIS; GENETIC DISTANCE; GENETIC RECOMBINATION; GEOMETRY; HEPATITIS B VIRUS; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; VIRUS ISOLATION; YEAST; BIOLOGICAL MODEL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM;

EID: 0036897646     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004030     Document Type: Article
Times cited : (124)

References (32)
  • 1
    • 0026911267 scopus 로고
    • Split decomposition: A new and useful approach to phylogenetic analysis of distance data
    • Bandelt, H.-J., and A. W. M Dress. 1992. Split decomposition: A new and useful approach to phylogenetic analysis of distance data. Mol. Phyl. Evol. 1:242-252.
    • (1992) Mol. Phyl. Evol. , vol.1 , pp. 242-252
    • Bandelt, H.-J.1    Dress, A.W.M.2
  • 2
    • 0029940859 scopus 로고    scopus 로고
    • Recombination between sequences of Hepatitis B virus from different genotypes
    • Bollyky, P. L., A. Rambaut, P. H. Harvey, and E. C. Holmes. 1996. Recombination between sequences of Hepatitis B virus from different genotypes. J. Mol. Evol. 42: 97-102.
    • (1996) J. Mol. Evol. , vol.42 , pp. 97-102
    • Bollyky, P.L.1    Rambaut, A.2    Harvey, P.H.3    Holmes, E.C.4
  • 3
    • 0002074731 scopus 로고
    • The recovery of trees from measures of dissimilarity
    • F. R. Hodson, D. G. Kendall, and P. Tautu, eds. Edinburgh University Press, Edinburgh, U.K
    • Buneman, P. 1971. The recovery of trees from measures of dissimilarity. Pp. 387-395 in F. R. Hodson, D. G. Kendall, and P. Tautu, eds. Mathematics in the Archaeological and Historical Sciences. Edinburgh University Press, Edinburgh, U.K.
    • (1971) Mathematics in the Archaeological and Historical Sciences , pp. 387-395
    • Buneman, P.1
  • 4
    • 26544445783 scopus 로고
    • Statistische geometrie von konfigurationen und deren evolution in sequenz-räumen - Definitionen und probleme. Ein programmvorschlag
    • H. Begehr, ed. Kolloquium-Verlag, Berlin
    • Dress, A. 1988. Statistische geometrie von konfigurationen und deren evolution in sequenz-räumen - Definitionen und probleme. Ein programmvorschlag. In H. Begehr, ed. Die Bedentung der von Berlin Ausgehenden Mathematik in Vergangenheit und Gegenwart. Kolloquium-Verlag, Berlin.
    • (1988) Die Bedentung der von Berlin Ausgehenden Mathematik in Vergangenheit und Gegenwart
    • Dress, A.1
  • 5
    • 0025267881 scopus 로고
    • Statistical geometry on sequence space
    • Eigen, M., and R. Winkler-Oswatitsch. 1990. Statistical geometry on sequence space. Methods Enzymol. 183:505-530.
    • (1990) Methods Enzymol. , vol.183 , pp. 505-530
    • Eigen, M.1    Winkler-Oswatitsch, R.2
  • 6
    • 0024061028 scopus 로고
    • Statistical geometry in sequence space: A method of quantitative sequence analysis
    • Eigen, M., R. Winkler-Oswatitsch, and A. Dress. 1988. Statistical geometry in sequence space: A method of quantitative sequence analysis. Proc. Natl. Acad. Sci. USA. 85: 5913-5917.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 5913-5917
    • Eigen, M.1    Winkler-Oswatitsch, R.2    Dress, A.3
  • 7
    • 0000461280 scopus 로고
    • Confidence-limits on phylogenies - An approach using the bootstrap
    • _, 1985. Confidence-limits on phylogenies - An approach using the bootstrap. Evolution 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
  • 9
    • 0029914127 scopus 로고    scopus 로고
    • Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination
    • Graser, Y., M. Volovsek, J. Arrington, G. Schonian, W. Presber, T. G. Mitchell, and R. Vilgalys. 1996. Molecular markers reveal that population structure of the human pathogen Candida albicans exhibits both clonality and recombination. Proc. Nat. Acad. Sci. 93:12473-12477.
    • (1996) Proc. Nat. Acad. Sci. , vol.93 , pp. 12473-12477
    • Graser, Y.1    Volovsek, M.2    Arrington, J.3    Schonian, G.4    Presber, W.5    Mitchell, T.G.6    Vilgalys, R.7
  • 10
    • 0031041347 scopus 로고    scopus 로고
    • A likelihood method for the detection of selection and recombination using sequence data
    • Grassly, N. C., and E. C. Holmes. 1997. A likelihood method for the detection of selection and recombination using sequence data. Mol. Biol. Evol. 14:239-247.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 239-247
    • Grassly, N.C.1    Holmes, E.C.2
  • 11
    • 21144475766 scopus 로고
    • Spectral analysis of phylogenetic data
    • Hendy, M. D., and D. Penny. 1993. Spectral analysis of phylogenetic data. J. Class. 10:5-24.
    • (1993) J. Class. , vol.10 , pp. 5-24
    • Hendy, M.D.1    Penny, D.2
  • 13
    • 0033021298 scopus 로고    scopus 로고
    • Phylogenetic evidence for recombination in Dengue virus
    • Holmes, E. C., M. Worobey, and A. Rambaut. 1999. Phylogenetic evidence for recombination in Dengue virus. Mol. Biol. Evol. 16:405-409.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 405-409
    • Holmes, E.C.1    Worobey, M.2    Rambaut, A.3
  • 14
    • 0031678692 scopus 로고    scopus 로고
    • SplitsTree: A program for analyzing and visualizing evolutionary data
    • Huson, D. 1998. SplitsTree: A program for analyzing and visualizing evolutionary data. Bioinformatics 14:68-73.
    • (1998) Bioinformatics , vol.14 , pp. 68-73
    • Huson, D.1
  • 15
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary of base substitution through comparative studies of nucleotide sequences
    • Kimura, M. 1980. A simple method for estimating evolutionary of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
    • (1980) J. Mol. Evol. , vol.16 , pp. 111-120
    • Kimura, M.1
  • 16
    • 0030000952 scopus 로고    scopus 로고
    • Relative Apparent Synapomorphy Analysis (RASA) I: The statistical measurement of phylogenetic signal
    • Lyons-weiler, J., G. A. Hoelzer, and R. J. Tausch. 1996. Relative Apparent Synapomorphy Analysis (RASA) I: The statistical measurement of phylogenetic signal. Mol. Biol. Evol. 13:749-757.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 749-757
    • Lyons-Weiler, J.1    Hoelzer, G.A.2    Tausch, R.J.3
  • 17
    • 0030732297 scopus 로고    scopus 로고
    • A graphical method for detecting recombination in phylogenetic data sets
    • Mcguire. G., E Wright, and M. J. Prentice. 1997. A graphical method for detecting recombination in phylogenetic data sets. Mol. Biol. Evol. 14:1125-1131.
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 1125-1131
    • Mcguire, G.1    Wright, E.2    Prentice, M.J.3
  • 18
    • 0034942558 scopus 로고    scopus 로고
    • Quartetmapping, a generalization of the likelihood-mapping procedure
    • Nieselt-Struwe, K., and A. Von Haeseler. 2001. Quartetmapping, a generalization of the likelihood-mapping procedure. Mol. Biol. Evol. 18:1204-1219.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1204-1219
    • Nieselt-Struwe, K.1    Von Haeseler, A.2
  • 19
    • 0035139147 scopus 로고    scopus 로고
    • Intraspecific gene genealogies: Trees grafting into networks
    • Posada, D., and K. A. Crandall. 2001 Intraspecific gene genealogies: Trees grafting into networks. Trends Ecol. Evol. 16(1):37-45.
    • (2001) Trends Ecol. Evol. , vol.16 , Issue.1 , pp. 37-45
    • Posada, D.1    Crandall, K.A.2
  • 20
    • 0027515402 scopus 로고
    • The yeast Candida albicans has a clonal mode of reproduction in a population of infected human immunodeficiency virus-positive patients
    • Pujol, C., J. Reynes, E Renaud, M. Raymond, M. Tibayrenc, E J. Ayala, E Janbon, M. Mallie, and J. Bastide. 1993. The yeast Candida albicans has a clonal mode of reproduction in a population of infected human immunodeficiency virus-positive patients. Proc. Nat. Acad. Sci. 90: 9456-9459.
    • (1993) Proc. Nat. Acad. Sci. , vol.90 , pp. 9456-9459
    • Pujol, C.1    Reynes, J.2    Renaud, E.3    Raymond, M.4    Tibayrenc, M.5    Ayala, E.J.6    Janbon, E.7    Mallie, M.8    Bastide, J.9
  • 21
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A. E., and N. C. Grassly. 1997. Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1:235-238.
    • (1997) Comput. Appl. Biosci. , vol.1 , pp. 235-238
    • Rambaut, A.E.1    Grassly, N.C.2
  • 23
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 24
    • 0033677382 scopus 로고    scopus 로고
    • Early eukaryote evolution based on mitochondrial gene order breakpoints
    • Sankoff, D., D. Bryant, M. Denault, B. E Lang, and G. Burger. 2000. Early eukaryote evolution based on mitochondrial gene order breakpoints. J. Comp. Biol. 7:521-536.
    • (2000) J. Comp. Biol. , vol.7 , pp. 521-536
    • Sankoff, D.1    Bryant, D.2    Denault, M.3    Lang, B.E.4    Burger, G.5
  • 25
    • 0032877706 scopus 로고    scopus 로고
    • Evidence for a general-purpose genotype in Candida albicans, highly prevalent in multiple geographical regions, patient types and types of infection
    • Schmid, J., S. Herd, P. R. Hunter, R. D. Cannon, and M. Salleh. 1999. Evidence for a general-purpose genotype in Candida albicans, highly prevalent in multiple geographical regions, patient types and types of infection. Microbiology 145:2405-2413.
    • (1999) Microbiology , vol.145 , pp. 2405-2413
    • Schmid, J.1    Herd, S.2    Hunter, P.R.3    Cannon, R.D.4    Salleh, M.5
  • 26
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
    • Strimmer, K., and A. Von Haeseler. 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 27
    • 0031002417 scopus 로고    scopus 로고
    • Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment
    • _, 1997. Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sci. USA. 94:6815-6819.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 6815-6819
  • 29
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D. M. Hillis, C. Moritz, and B. K. Mable, eds. Sinauer Associates, Sunderland, Mass
    • Swofford, D., G. Olsen, P. Waddell, and D. Hillis. 1996. Phylogenetic inference. Pp. 407-514 in D. M. Hillis, C. Moritz, and B. K. Mable, eds. Molecular Systematics. 2nd Edition. Sinauer Associates, Sunderland, Mass.
    • (1996) Molecular Systematics. 2nd Edition , pp. 407-514
    • Swofford, D.1    Olsen, G.2    Waddell, P.3    Hillis, D.4
  • 30
    • 0031184310 scopus 로고    scopus 로고
    • Are Candida albicans natural populations subdivided?
    • Tibayrenc, M. 1997. Are Candida albicans natural populations subdivided? Trends Microbiol. 5:253-257.
    • (1997) Trends Microbiol. , vol.5 , pp. 253-257
    • Tibayrenc, M.1
  • 31
    • 0031892518 scopus 로고    scopus 로고
    • Phylogenetic profiles: A graphical method for detecting genetic recombinations in homologous sequences
    • Weiller, G. E 1998. Phylogenetic profiles: A graphical method for detecting genetic recombinations in homologous sequences. Mol. Evol. Sys. 15:326-335.
    • (1998) Mol. Evol. Sys. , vol.15 , pp. 326-335
    • Weiller, G.E.1
  • 32
    • 0002275128 scopus 로고
    • Reconstruction of a tree from the distances between its pendant vertices
    • Zaretsky, K. 1965. Reconstruction of a tree from the distances between its pendant vertices. Uspekhi Math. Nauk (Russian Mathematical Surveys) 20:90-92.
    • (1965) Uspekhi Math. Nauk (Russian Mathematical Surveys) , vol.20 , pp. 90-92
    • Zaretsky, K.1


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