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Volumn 13, Issue 8, 2006, Pages 1397-1418

On the repeat-annotated phylogenetic tree reconstruction problem

Author keywords

Genome rearrangements; Phylogenetic inference; Repmaps; Set tries

Indexed keywords

ALGORITHM; ARTICLE; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; GENETIC RECOMBINATION; GENETICS; METHODOLOGY; NUCLEOTIDE REPEAT; PHYLOGENY;

EID: 39049177460     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2006.13.1397     Document Type: Article
Times cited : (2)

References (53)
  • 2
    • 0042318548 scopus 로고    scopus 로고
    • Associations between inverted repeats and the structural evolution of bacterial genomes
    • Achaz, G., Coissac, E., Netter, P., et al. 2003. Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics 164, 1279-1289.
    • (2003) Genetics , vol.164 , pp. 1279-1289
    • Achaz, G.1    Coissac, E.2    Netter, P.3
  • 3
    • 0034767147 scopus 로고    scopus 로고
    • A linear-time algorithm for computing inversion distance between signed permutations with an experimental study
    • Bader, D.A., Moret, B.M.E., and Yan, M. 2001. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8, 483-491.
    • (2001) J. Comput. Biol , vol.8 , pp. 483-491
    • Bader, D.A.1    Moret, B.M.E.2    Yan, M.3
  • 4
    • 0030130366 scopus 로고    scopus 로고
    • Genome rearrangements and sorting by reversals
    • Bafna, V., and Pevzner, P.A. 1996. Genome rearrangements and sorting by reversals. SIAM J. Comput. 25, 272-289.
    • (1996) SIAM J. Comput , vol.25 , pp. 272-289
    • Bafna, V.1    Pevzner, P.A.2
  • 7
    • 11844251253 scopus 로고    scopus 로고
    • A very elementary presentation of the Hannenhalli-Pevzner theory
    • Bergeron, A. 2005. A very elementary presentation of the Hannenhalli-Pevzner theory. Discrete Appl. Math. 146, 134-145.
    • (2005) Discrete Appl. Math , vol.146 , pp. 134-145
    • Bergeron, A.1
  • 8
    • 10044294457 scopus 로고    scopus 로고
    • Common intervals and sorting by reversals: A marriage of necessity
    • Bergeron, A., Heber, S., and Stoye, J. 2002. Common intervals and sorting by reversals: a marriage of necessity. Bioinformatics 18, S54-S63.
    • (2002) Bioinformatics , vol.18
    • Bergeron, A.1    Heber, S.2    Stoye, J.3
  • 12
    • 0036143403 scopus 로고    scopus 로고
    • Genome-scale evolution: Reconstructing gene orders in the ancestral species
    • Bourque, G., and Pevzner, P.A. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26-36.
    • (2002) Genome Res , vol.12 , pp. 26-36
    • Bourque, G.1    Pevzner, P.A.2
  • 13
    • 12744263078 scopus 로고    scopus 로고
    • Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages
    • Bourque, G., Zdobnov, E.M., Bork, P., et al. 2005. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15, 98-110.
    • (2005) Genome Res , vol.15 , pp. 98-110
    • Bourque, G.1    Zdobnov, E.M.2    Bork, P.3
  • 14
    • 0035201828 scopus 로고    scopus 로고
    • Phylogenetic inferences from molecular sequences: Review and critique
    • Brocchieri, L. 2001. Phylogenetic inferences from molecular sequences: review and critique. Theoret. Popul. Biol. 59, 27-40.
    • (2001) Theoret. Popul. Biol , vol.59 , pp. 27-40
    • Brocchieri, L.1
  • 15
    • 0035902443 scopus 로고    scopus 로고
    • Instability of repetitive DNA sequences: The role of replication in multiple mechanisms
    • Bzymek, M., and Lovett, S.T. 2001. Instability of repetitive DNA sequences: the role of replication in multiple mechanisms. Proc. Natl. Acad. Sci. USA 98, 8319-8325.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 8319-8325
    • Bzymek, M.1    Lovett, S.T.2
  • 16
    • 0032635206 scopus 로고    scopus 로고
    • Formulations and hardness of multiple sorting by reversals
    • Caprara, A. 1999. Formulations and hardness of multiple sorting by reversals. Proc 3th Ann. Int. Conf. Comput. Mol. Biol. 84-93.
    • (1999) Proc 3th Ann. Int. Conf. Comput. Mol. Biol , pp. 84-93
    • Caprara, A.1
  • 17
    • 0039577309 scopus 로고    scopus 로고
    • Sorting with fixed-length reversals
    • Chen, T., and Skiena, S. 1996. Sorting with fixed-length reversals. Discrete Appl. Math. 71, 79-95.
    • (1996) Discrete Appl. Math , vol.71 , pp. 79-95
    • Chen, T.1    Skiena, S.2
  • 18
    • 0242659445 scopus 로고    scopus 로고
    • Sorting strings by reversals and by transpositions
    • Christie, D.A., and Irving, R.W. 2001. Sorting strings by reversals and by transpositions. SIAM J. Discrete Math. 14, 193-206.
    • (2001) SIAM J. Discrete Math , vol.14 , pp. 193-206
    • Christie, D.A.1    Irving, R.W.2
  • 19
    • 0037161811 scopus 로고    scopus 로고
    • Comparison of the genomes of two Xanthomonas pathogens with differing host specificities
    • da Silva, A.C.R., Ferro, J.A., Reinach, F.C., et al. 2002. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417, 459-463.
    • (2002) Nature , vol.417 , pp. 459-463
    • da Silva, A.C.R.1    Ferro, J.A.2    Reinach, F.C.3
  • 20
    • 84976808645 scopus 로고
    • Data structures and algorithms for disjoint set union problems
    • Galil, Z., and Italiano, G. F. 1991. Data structures and algorithms for disjoint set union problems. ACM Comput. Surv. 23, 319-344.
    • (1991) ACM Comput. Surv , vol.23 , pp. 319-344
    • Galil, Z.1    Italiano, G.F.2
  • 22
    • 0000840830 scopus 로고    scopus 로고
    • A 2-approximation algorithm for genome rearrangements by reversals and transpositions
    • Gu, Q.-P., Peng, S., and Sudborough, I. 1999. A 2-approximation algorithm for genome rearrangements by reversals and transpositions. Theoret. Comput. Sci. 210, 327-339.
    • (1999) Theoret. Comput. Sci , vol.210 , pp. 327-339
    • Gu, Q.-P.1    Peng, S.2    Sudborough, I.3
  • 23
    • 0002856077 scopus 로고    scopus 로고
    • Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals
    • Hannenhalli, S., and Pevzner, P.A. 1999. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM 46, 1-27.
    • (1999) J. ACM , vol.46 , pp. 1-27
    • Hannenhalli, S.1    Pevzner, P.A.2
  • 25
    • 35048840656 scopus 로고    scopus 로고
    • A 1.5-approximation algorithm for sorting by transpositions and transreversals
    • Hartman, T., and Sharan, R. 2004. A 1.5-approximation algorithm for sorting by transpositions and transreversals. Proc. 4th Workshop Algorithms Bioinformatics 50-61.
    • (2004) Proc. 4th Workshop Algorithms Bioinformatics , pp. 50-61
    • Hartman, T.1    Sharan, R.2
  • 26
    • 33746683240 scopus 로고    scopus 로고
    • Hughes, D. 2000. Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol. 1, reviews0006.1-0006.8.
    • Hughes, D. 2000. Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes. Genome Biol. 1, reviews0006.1-0006.8.
  • 28
    • 84976632165 scopus 로고
    • Exact and approximation algorithms for the inversion distance between two permutations
    • Kececioglu, J., and Sankoff, D. 1993. Exact and approximation algorithms for the inversion distance between two permutations. Lect. Notes Comput. Sci. 684, 87-105.
    • (1993) Lect. Notes Comput. Sci , vol.684 , pp. 87-105
    • Kececioglu, J.1    Sankoff, D.2
  • 29
    • 84896575459 scopus 로고
    • Efficient bounds for oriented chromosome inversion distance
    • Kececioglu, J., and Sankoff, D. 1994. Efficient bounds for oriented chromosome inversion distance. Lect. Notes Comput. Sci. 807, 307-325.
    • (1994) Lect. Notes Comput. Sci , vol.807 , pp. 307-325
    • Kececioglu, J.1    Sankoff, D.2
  • 30
    • 0028102267 scopus 로고
    • Biochemistry of homologous recombination in Escherichia coli
    • Kowalczykowski, S.C., Dixon, D.A., Eggleston, A.K., et al. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58, 401-465.
    • (1994) Microbiol. Rev , vol.58 , pp. 401-465
    • Kowalczykowski, S.C.1    Dixon, D.A.2    Eggleston, A.K.3
  • 31
    • 0035997347 scopus 로고    scopus 로고
    • The bacterial RecA protein and the recombinational DNA repair of stalled replication forks
    • Lusetti, S.L., and Cox, M.M. 2002. The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Ann. Rev. Biochem. 71, 71-100.
    • (2002) Ann. Rev. Biochem , vol.71 , pp. 71-100
    • Lusetti, S.L.1    Cox, M.M.2
  • 33
    • 0037126071 scopus 로고    scopus 로고
    • Evolutionary analysis of arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
    • Martin, W., Rujan, T., Richly, E., et al. 2002. Evolutionary analysis of arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl. Acad. Sci. USA 99, 12246-12251.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12246-12251
    • Martin, W.1    Rujan, T.2    Richly, E.3
  • 35
    • 0042355274 scopus 로고    scopus 로고
    • Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica
    • Parkhill, J., Sebaihia, M., Preston, A., et al. 2003. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35, 32-40.
    • (2003) Nat. Genet , vol.35 , pp. 32-40
    • Parkhill, J.1    Sebaihia, M.2    Preston, A.3
  • 36
    • 33645766047 scopus 로고    scopus 로고
    • The fragile breakage versus random breakage models of chromosome evolution
    • Peng, Q., Pevzner, P.A., and Tesler, G. 2006. The fragile breakage versus random breakage models of chromosome evolution. PLoS Computational Biology 2, e14.
    • (2006) PLoS Computational Biology , vol.2
    • Peng, Q.1    Pevzner, P.A.2    Tesler, G.3
  • 37
    • 0037264074 scopus 로고    scopus 로고
    • Genome rearrangements in mammalian evolution: Lessons from human and mouse genomes
    • Pevzner, P.A., and Tesler, G. 2003. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res. 13, 37-45.
    • (2003) Genome Res , vol.13 , pp. 37-45
    • Pevzner, P.A.1    Tesler, G.2
  • 38
    • 22344455805 scopus 로고    scopus 로고
    • Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris
    • Qian, W., Jia, Y., Ren, S.-X., et al. 2005. Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res. 15, 757-767.
    • (2005) Genome Res , vol.15 , pp. 757-767
    • Qian, W.1    Jia, Y.2    Ren, S.-X.3
  • 39
    • 0037803483 scopus 로고    scopus 로고
    • An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: From duplications to genome reduction
    • Rocha, E.P.C. 2003a. An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction. Genome Res. 13, 1123-1132.
    • (2003) Genome Res , vol.13 , pp. 1123-1132
    • Rocha, E.P.C.1
  • 40
    • 0242380287 scopus 로고    scopus 로고
    • DNA repeats lead to the accelerated loos of gene order in bacteria
    • Rocha, E.P.C. 2003b. DNA repeats lead to the accelerated loos of gene order in bacteria. Trends Genet. 19, 600-603.
    • (2003) Trends Genet , vol.19 , pp. 600-603
    • Rocha, E.P.C.1
  • 41
    • 4644309277 scopus 로고    scopus 로고
    • Order and disorder in bacterial genomes
    • Rocha, E.P.C. 2004. Order and disorder in bacterial genomes. Curr. Opin. Microbiol. 7, 519-537.
    • (2004) Curr. Opin. Microbiol , vol.7 , pp. 519-537
    • Rocha, E.P.C.1
  • 42
    • 0033397546 scopus 로고    scopus 로고
    • Functional and evolutionary roles of long repeats in prokaryotes
    • Rocha, E.P.C., Danchin, A., and Viari, A. 1999. Functional and evolutionary roles of long repeats in prokaryotes. Res. Microbiol. 150, 725-733.
    • (1999) Res. Microbiol , vol.150 , pp. 725-733
    • Rocha, E.P.C.1    Danchin, A.2    Viari, A.3
  • 43
    • 0033954246 scopus 로고    scopus 로고
    • Rothstein, R., Michel, B., and Gangloff, S. 2000. Replication fork pausing and recombination or gimme a break. Genes Dev. 14, 1-10.
    • Rothstein, R., Michel, B., and Gangloff, S. 2000. Replication fork pausing and recombination or "gimme a break." Genes Dev. 14, 1-10.
  • 44
    • 0345447448 scopus 로고    scopus 로고
    • Rearrangements and chromosomal evolution
    • Sankoff, D. 2003. Rearrangements and chromosomal evolution. Curr. Opin. Genet. Dev. 13, 583-587.
    • (2003) Curr. Opin. Genet. Dev , vol.13 , pp. 583-587
    • Sankoff, D.1
  • 45
    • 0031721577 scopus 로고    scopus 로고
    • Multiple genome rearrangement and breakpoint phylogeny
    • Sankoff, D., and Blanchette, M. 1998. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5, 555-570.
    • (1998) J. Comput. Biol , vol.5 , pp. 555-570
    • Sankoff, D.1    Blanchette, M.2
  • 46
    • 23844460187 scopus 로고    scopus 로고
    • Chromosomal breakpoint reuse in genome sequence rearrangement
    • Sankoff, D., and Trinh, P. 2005. Chromosomal breakpoint reuse in genome sequence rearrangement. J. Comput. Biol. 12, 812-821.
    • (2005) J. Comput. Biol , vol.12 , pp. 812-821
    • Sankoff, D.1    Trinh, P.2
  • 47
    • 0024919121 scopus 로고
    • Homologous recombination in prokaryotes: Enzymes and controlling sites
    • Smith, G.R. 1989. Homologous recombination in prokaryotes: enzymes and controlling sites. Genome 31, 520-527.
    • (1989) Genome , vol.31 , pp. 520-527
    • Smith, G.R.1
  • 48
    • 35048854608 scopus 로고    scopus 로고
    • Sorting by length-weighted reversals: Dealing with signs and circularity
    • Swidan, F., Bender, M.A., Ge, D., et al. 2004. Sorting by length-weighted reversals: dealing with signs and circularity. Lect. Notes Comput. Sci. 3109, 32-46.
    • (2004) Lect. Notes Comput. Sci , vol.3109 , pp. 32-46
    • Swidan, F.1    Bender, M.A.2    Ge, D.3
  • 49
    • 33748090605 scopus 로고    scopus 로고
    • An integrative method for accurate comparative genome mapping
    • Swidan, F., Rocha, E.P.C., Shmoish, M., et al. 2006. An integrative method for accurate comparative genome mapping. PLoS Comput. Biol. 2, e75.
    • (2006) PLoS Comput. Biol , vol.2
    • Swidan, F.1    Rocha, E.P.C.2    Shmoish, M.3
  • 50
    • 35048862957 scopus 로고    scopus 로고
    • Sorting by reversals in subquadratic time
    • Tannier, E., and Sagot, M.-F. 2004. Sorting by reversals in subquadratic time. Lect. Notes Comput. Sci. 3109, 1-13.
    • (2004) Lect. Notes Comput. Sci , vol.3109 , pp. 1-13
    • Tannier, E.1    Sagot, M.-F.2
  • 51
    • 24744467149 scopus 로고    scopus 로고
    • Genomic features in the breakpoint regions between syntenic blocks
    • Trinh, P., McLysaght, A., and Sankoff, D. 2004. Genomic features in the breakpoint regions between syntenic blocks. Bioinformatics 20, i318-i325.
    • (2004) Bioinformatics , vol.20
    • Trinh, P.1    McLysaght, A.2    Sankoff, D.3
  • 53
    • 0348044549 scopus 로고    scopus 로고
    • Genome trees constructed using five different approaches suggest new major bacterial clades
    • Wolf, Y., Rogozin, I., Grishin, N., et al. 2001. Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1, 1-8.
    • (2001) BMC Evol. Biol , vol.1 , pp. 1-8
    • Wolf, Y.1    Rogozin, I.2    Grishin, N.3


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