메뉴 건너뛰기




Volumn 46, Issue 11, 2014, Pages 1205-1211

Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BAYES THEOREM; BIOLOGICAL MODEL; DNA SEQUENCE; EPIDEMIC; EPIDEMIOLOGY; GENETIC RECOMBINATION; GENETICS; GENOMICS; HUMAN; LEGIONELLA PNEUMOPHILA; LEGIONNAIRES' DISEASE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SPAIN; STATISTICAL MODEL;

EID: 84908868800     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3114     Document Type: Article
Times cited : (61)

References (66)
  • 2
    • 70149105095 scopus 로고    scopus 로고
    • The population and evolutionary dynamics of homologous gene recombination in bacteria
    • Levin, B.R. &Cornejo, O.E. The population and evolutionary dynamics of homologous gene recombination in bacteria. PLoS Genet. 5, e1000601 (2009).
    • (2009) PLoS Genet , vol.5 , pp. e1000601
    • Levin, B.R.1    Cornejo, O.E.2
  • 3
    • 84875626143 scopus 로고    scopus 로고
    • Assessing the probability of detection of horizontal gene transfer events in bacterial populations
    • Townsend, J.P., Bhn, T. &Nielsen, K.M. Assessing the probability of detection of horizontal gene transfer events in bacterial populations. Front. Microbiol. 3, 27 (2012).
    • (2012) Front. Microbiol , vol.3 , pp. 27
    • Townsend, J.P.1    Bhn, T.2    Nielsen, K.M.3
  • 4
    • 0034691077 scopus 로고    scopus 로고
    • Bacteria are different: Observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes
    • Levin, B.R. &Bergstrom, C.T. Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc. Natl. Acad. Sci. USA 97, 6981-6985 (2000).
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 6981-6985
    • Levin, B.R.1    Bergstrom, C.T.2
  • 5
    • 33751558792 scopus 로고    scopus 로고
    • Evolutionary history of Salmonella typhi
    • Roumagnac, P. et al. Evolutionary history of Salmonella typhi. Science 314, 1301-1304 (2006).
    • (2006) Science , vol.314 , pp. 1301-1304
    • Roumagnac, P.1
  • 6
    • 84875908238 scopus 로고    scopus 로고
    • Antibiotic resistance shaping multilevel population biology of bacteria
    • Baquero, F., Tedim, A.S. &Coque, T.M. Antibiotic resistance shaping multilevel population biology of bacteria. Front. Microbiol. 4, 15 (2013).
    • (2013) Front. Microbiol , vol.4 , pp. 15
    • Baquero, F.1    Tedim, A.S.2    Coque, T.M.3
  • 7
    • 78650854393 scopus 로고    scopus 로고
    • The origin of the Haitian cholera outbreak strain
    • Chin, C.S. et al. The origin of the Haitian cholera outbreak strain. N. Engl. J. Med. 364, 33-42 (2011).
    • (2011) N. Engl. J. Med , vol.364 , pp. 33-42
    • Chin, C.S.1
  • 8
    • 79251544864 scopus 로고    scopus 로고
    • Rapid pneumococcal evolution in response to clinical interventions
    • Croucher, N.J. et al. Rapid pneumococcal evolution in response to clinical interventions. Science 331, 430-434 (2011).
    • (2011) Science , vol.331 , pp. 430-434
    • Croucher, N.J.1
  • 9
    • 79951995822 scopus 로고    scopus 로고
    • Whole-genome squencing and social-network analysis of a tuberculosis outbreak
    • Gardy, J.L. et al. Whole-genome squencing and social-network analysis of a tuberculosis outbreak. N. Engl. J. Med. 364, 730-739 (2011).
    • (2011) N. Engl. J. Med , vol.364 , pp. 730-739
    • Gardy, J.L.1
  • 10
    • 79960609901 scopus 로고    scopus 로고
    • Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104: H4 outbreak by rapid next generation sequencing technology
    • Mellmann, A. et al. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104: H4 outbreak by rapid next generation sequencing technology. PLoS ONE 6, e22751 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e22751
    • Mellmann, A.1
  • 11
    • 84862199752 scopus 로고    scopus 로고
    • Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak
    • Köser, C.U. et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N. Engl. J. Med. 366, 2267-2275 (2012).
    • (2012) N. Engl. J. Med , vol.366 , pp. 2267-2275
    • Köser, C.U.1
  • 12
    • 84872515273 scopus 로고    scopus 로고
    • Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: A descriptive study
    • Harris, S.R. et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect. Dis. 13, 130-136 (2013).
    • (2013) Lancet Infect. Dis , vol.13 , pp. 130-136
    • Harris, S.R.1
  • 13
    • 0036314980 scopus 로고    scopus 로고
    • Legionella and Legionnaires disease: 25 years of investigation
    • Fields, B.S., Benson, R.F. &Besser, R.E. Legionella and Legionnaires disease: 25 years of investigation. Clin. Microbiol. Rev. 15, 506-526 (2002).
    • (2002) Clin. Microbiol. Rev , vol.15 , pp. 506-526
    • Fields, B.S.1    Benson, R.F.2    Besser, R.E.3
  • 14
    • 0017726281 scopus 로고
    • Legionnaires disease: Description of an epidemic of pneumonia
    • Fraser, D.W. et al. Legionnaires disease: description of an epidemic of pneumonia. N. Engl. J. Med. 297, 1189-1197 (1977).
    • (1977) N. Engl. J. Med , vol.297 , pp. 1189-1197
    • Fraser, D.W.1
  • 17
    • 80054707563 scopus 로고    scopus 로고
    • Cluster of travel-associated Legionnaires disease in Lazise, Italy, July to August 2011
    • Rota, M. et al. Cluster of travel-associated Legionnaires disease in Lazise, Italy, July to August 2011. Euro Surveill. 16, 19982 (2011).
    • (2011) Euro Surveill , vol.16 , pp. 19982
    • Rota, M.1
  • 18
    • 84878820895 scopus 로고    scopus 로고
    • First outbreak of nosocomial Legionella infection in term neonates caused by a cold mist ultrasonic humidifier
    • Yiallouros, P.K. et al. First outbreak of nosocomial Legionella infection in term neonates caused by a cold mist ultrasonic humidifier. Clin. Infect. Dis. 57, 48-56 (2013).
    • (2013) Clin. Infect. Dis , vol.57 , pp. 48-56
    • Yiallouros, P.K.1
  • 19
    • 78049494186 scopus 로고    scopus 로고
    • A community outbreak of Legionnaires disease in South Wales, August-September 2010
    • Keramarou, M. &Evans, M.R. A community outbreak of Legionnaires disease in South Wales, August-September 2010. Euro Surveill. 15, 19691 (2010).
    • (2010) Euro Surveill , vol.15 , pp. 19691
    • Keramarou, M.1    Evans, M.R.2
  • 20
    • 84866706759 scopus 로고    scopus 로고
    • An outbreak of Legionnaires disease associated with a display spa pool in retail premises, Stoke-on-Trent, United Kingdom, July 2012
    • Coetzee, N. et al. An outbreak of Legionnaires disease associated with a display spa pool in retail premises, Stoke-on-Trent, United Kingdom, July 2012. Euro Surveill. 17, 20271 (2012).
    • (2012) Euro Surveill , vol.17 , pp. 20271
    • Coetzee, N.1
  • 21
    • 84864338891 scopus 로고    scopus 로고
    • Public health response to an outbreak of Legionnaires disease in Edinburgh, United Kingdom, June 2012
    • McCormick, D. et al. Public health response to an outbreak of Legionnaires disease in Edinburgh, United Kingdom, June 2012. Euro Surveill. 17, 20216 (2012).
    • (2012) Euro Surveill , vol.17 , pp. 20216
    • McCormick, D.1
  • 22
    • 0037493255 scopus 로고    scopus 로고
    • Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation
    • Gaia, V., Fry, N.K., Harrison, T.J. &Peduzzi, R. Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation. J. Clin. Microbiol. 41, 2932-2939 (2003).
    • (2003) J. Clin. Microbiol , vol.41 , pp. 2932-2939
    • Gaia, V.1    Fry, N.K.2    Harrison, T.J.3    Peduzzi, R.4
  • 23
    • 18544387792 scopus 로고    scopus 로고
    • Consensus sequence-based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila
    • Gaia, V. et al. Consensus sequence-based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila. J. Clin. Microbiol. 43, 2047-2052 (2005).
    • (2005) J. Clin. Microbiol , vol.43 , pp. 2047-2052
    • Gaia, V.1
  • 24
    • 34250678922 scopus 로고    scopus 로고
    • Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence-based scheme for typing Legionella pneumophila serogroup 1 strains
    • Ratzow, S., Gaia, V., Helbig, J.H., Fry, N.K. &Luck, P.C. Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence-based scheme for typing Legionella pneumophila serogroup 1 strains. J. Clin. Microbiol. 45, 1965-1968 (2007).
    • (2007) J. Clin. Microbiol , vol.45 , pp. 1965-1968
    • Ratzow, S.1    Gaia, V.2    Helbig, J.H.3    Fry, N.K.4    Luck, P.C.5
  • 25
    • 84904913266 scopus 로고    scopus 로고
    • Extension of the Legionella pneumophila sequence-based typing scheme to include strains carrying a variant of the N-acylneuraminate cytidylyltransferase gene
    • Mentasti, M. et al. Extension of the Legionella pneumophila sequence-based typing scheme to include strains carrying a variant of the N-acylneuraminate cytidylyltransferase gene. Clin. Microbiol. Infect. 20, O435-O441 (2014).
    • (2014) Clin. Microbiol. Infect , vol.20 , pp. O435-O441
    • Mentasti, M.1
  • 26
    • 78751561457 scopus 로고    scopus 로고
    • Quantifying nonvertical inheritance in the evolution of Legionella pneumophila
    • Coscollá, M., Comas, I. &González-Candelas, F. Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Mol. Biol. Evol. 28, 985-1001 (2011).
    • (2011) Mol. Biol. Evol , vol.28 , pp. 985-1001
    • Coscollá, M.1    Comas, I.2    González-Candelas, F.3
  • 27
    • 84878960447 scopus 로고    scopus 로고
    • Genome dynamics in legionella: The basis of versatility and adaptation to intracellular replication
    • Gomez-Valero, L. &Buchrieser, C. Genome dynamics in legionella: the basis of versatility and adaptation to intracellular replication. Cold Spring Harb. Perspect. Med. 3, a009993 (2013).
    • (2013) Cold Spring Harb. Perspect. Med , vol.3 , pp. a009993
    • Gomez-Valero, L.1    Buchrieser, C.2
  • 28
    • 84890837667 scopus 로고    scopus 로고
    • Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing
    • Underwood, A.P., Jones, G., Mentasti, M., Fry, N.K. &Harrison, T.G. Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing. BMC Microbiol. 13, 302 (2013).
    • (2013) BMC Microbiol , vol.13 , pp. 302
    • Underwood, A.P.1    Jones, G.2    Mentasti, M.3    Fry, N.K.4    Harrison, T.G.5
  • 29
    • 33846981510 scopus 로고    scopus 로고
    • Population structure and recombination in environmental isolates of Legionella pneumophila
    • Coscollá, M. &González-Candelas, F. Population structure and recombination in environmental isolates of Legionella pneumophila. Environ. Microbiol. 9, 643-656 (2007).
    • (2007) Environ. Microbiol , vol.9 , pp. 643-656
    • Coscollá, M.1    González-Candelas, F.2
  • 30
    • 79953172949 scopus 로고    scopus 로고
    • Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation
    • Rasko, D.A. et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc. Natl. Acad. Sci. USA 108, 5027-5032 (2011).
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 5027-5032
    • Rasko, D.A.1
  • 31
    • 84873467253 scopus 로고    scopus 로고
    • A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak
    • Reuter, S. et al. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ Open 3, e002175 (2013).
    • (2013) BMJ Open , vol.3 , pp. e002175
    • Reuter, S.1
  • 32
    • 84895858474 scopus 로고    scopus 로고
    • Dense genomic sampling identifies highways of pneumococcal recombination
    • Chewapreecha, C. et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat. Genet. 46, 305-309 (2014).
    • (2014) Nat. Genet , vol.46 , pp. 305-309
    • Chewapreecha, C.1
  • 33
    • 84878735463 scopus 로고    scopus 로고
    • Population genomics of post-vaccine changes in pneumococcal epidemiology
    • Croucher, N.J. et al. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat. Genet. 45, 656-663 (2013).
    • (2013) Nat. Genet , vol.45 , pp. 656-663
    • Croucher, N.J.1
  • 34
    • 84871990888 scopus 로고    scopus 로고
    • Emergence and global spread of epidemic healthcare-associated Clostridium difficile
    • He, M. et al. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat. Genet. 45, 109-113 (2013).
    • (2013) Nat. Genet , vol.45 , pp. 109-113
    • He, M.1
  • 35
    • 84865683817 scopus 로고    scopus 로고
    • Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
    • Holt, K.E. et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat. Genet. 44, 1056-1059 (2012).
    • (2012) Nat. Genet , vol.44 , pp. 1056-1059
    • Holt, K.E.1
  • 37
    • 84877584233 scopus 로고    scopus 로고
    • Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: A retrospective cohort study
    • Bryant, J.M. et al. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet 381, 1551-1560 (2013).
    • (2013) Lancet , vol.381 , pp. 1551-1560
    • Bryant, J.M.1
  • 38
    • 0033120547 scopus 로고    scopus 로고
    • Hypermutation in pathogenic bacteria: Frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype
    • Bucci, C. et al. Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype. Mol. Cell 3, 435-445 (1999).
    • (1999) Mol. Cell , vol.3 , pp. 435-445
    • Bucci, C.1
  • 39
    • 84865279338 scopus 로고    scopus 로고
    • General and inducible hypermutation facilitate parallel adaptation in Pseudomonas aeruginosa despite divergent mutation spectra
    • Weigand, M.R. &Sundin, G.W. General and inducible hypermutation facilitate parallel adaptation in Pseudomonas aeruginosa despite divergent mutation spectra. Proc. Natl. Acad. Sci. USA 109, 13680-13685 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 13680-13685
    • Weigand, M.R.1    Sundin, G.W.2
  • 40
    • 67149119196 scopus 로고    scopus 로고
    • Hyper-recombination, diversity, and antibiotic resistance in Pneumococcus
    • Hanage, W.P., Fraser, C., Tang, J., Connor, T.R. &Corander, J. Hyper-recombination, diversity, and antibiotic resistance in Pneumococcus. Science 324, 1454-1457 (2009).
    • (2009) Science , vol.324 , pp. 1454-1457
    • Hanage, W.P.1    Fraser, C.2    Tang, J.3    Connor, T.R.4    Corander, J.5
  • 41
    • 39449116981 scopus 로고    scopus 로고
    • A dominant clone of Leptospira interrogans associated with an outbreak of human leptospirosis in Thailand
    • Thaipadungpanit, J. et al. A dominant clone of Leptospira interrogans associated with an outbreak of human leptospirosis in Thailand. PLoS Negl. Trop. Dis. 1, e56 (2007).
    • (2007) PLoS Negl. Trop. Dis , vol.1 , pp. e56
    • Thaipadungpanit, J.1
  • 42
    • 45749090201 scopus 로고    scopus 로고
    • Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum
    • Nicolas, P. et al. Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl. Environ. Microbiol. 74, 3702-3709 (2008).
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 3702-3709
    • Nicolas, P.1
  • 43
    • 58549084151 scopus 로고    scopus 로고
    • A comparison of homologous recombination rates in bacteria and archaea
    • Vos, M. &Didelot, X. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3, 199-208 (2009).
    • (2009) ISME J , vol.3 , pp. 199-208
    • Vos, M.1    Didelot, X.2
  • 44
    • 22144486947 scopus 로고    scopus 로고
    • Fuzzy species among recombinogenic bacteria
    • Hanage, W.P., Fraser, C. &Spratt, B.G. Fuzzy species among recombinogenic bacteria. BMC Biol. 3, 6 (2005).
    • (2005) BMC Biol , vol.3 , pp. 6
    • Hanage, W.P.1    Fraser, C.2    Spratt, B.G.3
  • 45
    • 57349116172 scopus 로고    scopus 로고
    • Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae
    • Brochet, M. et al. Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae. Proc. Natl. Acad. Sci. USA 105, 15961-15966 (2008).
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 15961-15966
    • Brochet, M.1
  • 46
    • 77952168929 scopus 로고    scopus 로고
    • Evolutionary dynamics of Clostridium difficile over short and long time scales
    • He, M. et al. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl. Acad. Sci. USA 107, 7527-7532 (2010).
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 7527-7532
    • He, M.1
  • 47
    • 34547642553 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis nuoG is a virulence gene that inhibits apoptosis of infected host cells
    • Velmurugan, K. et al. Mycobacterium tuberculosis nuoG is a virulence gene that inhibits apoptosis of infected host cells. PLoS Pathog. 3, e110 (2007).
    • (2007) PLoS Pathog , vol.3 , pp. e110
    • Velmurugan, K.1
  • 48
    • 77954064664 scopus 로고    scopus 로고
    • The type i NADH dehydrogenase of Mycobacterium tuberculosis counters phagosomal NOX2 activity to inhibit TNF-α-mediated host cell apoptosis
    • Miller, J.L., Velmurugan, K., Cowan, M.J. &Briken, V. The type I NADH dehydrogenase of Mycobacterium tuberculosis counters phagosomal NOX2 activity to inhibit TNF-α-mediated host cell apoptosis. PLoS Pathog. 6, e1000864 (2010).
    • (2010) PLoS Pathog , vol.6 , pp. e1000864
    • Miller, J.L.1    Velmurugan, K.2    Cowan, M.J.3    Briken, V.4
  • 49
    • 84856003520 scopus 로고    scopus 로고
    • Mycobacterium tuberculosis inhibits neutrophil apoptosis, leading to delayed activation of naive CD4 T cells
    • Blomgran, R., Desvignes, L., Briken, V. &Ernst, J.D. Mycobacterium tuberculosis inhibits neutrophil apoptosis, leading to delayed activation of naive CD4 T cells. Cell Host Microbe 11, 81-90 (2012).
    • (2012) Cell Host Microbe , vol.11 , pp. 81-90
    • Blomgran, R.1    Desvignes, L.2    Briken, V.3    Ernst, J.D.4
  • 50
    • 66049089612 scopus 로고    scopus 로고
    • On the origin of prokaryotic species
    • Doolittle, W.F. &Zhaxybayeva, O. On the origin of prokaryotic species. Genome Res. 19, 744-756 (2009).
    • (2009) Genome Res , vol.19 , pp. 744-756
    • Doolittle, W.F.1    Zhaxybayeva, O.2
  • 51
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. &Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 52
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino, D.R. &Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821-829 (2008).
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 53
    • 74049108922 scopus 로고    scopus 로고
    • BLAST+: Architecture and applications
    • Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
    • (2009) BMC Bioinformatics , vol.10 , pp. 421
    • Camacho, C.1
  • 54
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 55
    • 84871227763 scopus 로고    scopus 로고
    • LoFreq: A sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets
    • Wilm, A. et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 40, 11189-11201 (2012).
    • (2012) Nucleic Acids Res , vol.40 , pp. 11189-11201
    • Wilm, A.1
  • 56
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • Darling, A.C.E., Mau, B., Blattner, F.R. &Perna, N.T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394-1403 (2004).
    • (2004) Genome Res , vol.14 , pp. 1394-1403
    • Darling, A.C.E.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 57
    • 77956193448 scopus 로고    scopus 로고
    • ProgressiveMauve: Multiple genome alignment with gene gain, loss and rearrangement
    • Darling, A.E., Mau, B. &Perna, N.T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5, e11147 (2010).
    • (2010) PLoS ONE , vol.5 , pp. e11147
    • Darling, A.E.1    Mau, B.2    Perna, N.T.3
  • 58
    • 67650757433 scopus 로고    scopus 로고
    • TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses
    • Capella-Gutiérrez, S., Silla-Martínez, J.M. &Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972-1973 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1972-1973
    • Capella-Gutiérrez, S.1    Silla-Martínez, J.M.2    Gabaldón, T.3
  • 59
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 60
    • 20744455231 scopus 로고    scopus 로고
    • VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data
    • Vilella, A.J., Blanco-Garcia, A., Hutter, S. &Rozas, J. VariScan: analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 21, 2791-2793 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 2791-2793
    • Vilella, A.J.1    Blanco-Garcia, A.2    Hutter, S.3    Rozas, J.4
  • 61
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739 (2011).
    • (2011) Mol. Biol. Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1
  • 62
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team R Foundation for Statistical Computing, Vienna
    • R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2011).
    • (2011) R: A Language and Environment for Statistical Computing
  • 63
    • 1042304216 scopus 로고    scopus 로고
    • APE: Analyses of Phylogenetics and Evolution in R language
    • Paradis, E., Claude, J. &Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20, 289-290 (2004).
    • (2004) Bioinformatics , vol.20 , pp. 289-290
    • Paradis, E.1    Claude, J.2    Strimmer, K.3
  • 64
    • 84864530626 scopus 로고    scopus 로고
    • Bayesian phylogenetics with BEAUti and the BEAST 1.7
    • Drummond, A.J., Suchard, M.A., Xie, D. &Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969-1973 (2012).
    • (2012) Mol. Biol. Evol , vol.29 , pp. 1969-1973
    • Drummond, A.J.1    Suchard, M.A.2    Xie, D.3    Rambaut, A.4
  • 65
    • 84872185929 scopus 로고    scopus 로고
    • Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis
    • Cui, Y. et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc. Natl. Acad. Sci. USA 110, 577-582 (2013).
    • (2013) Proc. Natl. Acad. Sci. USA , vol.110 , pp. 577-582
    • Cui, Y.1
  • 66
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H.A., Strimmer, K., Vingron, M. &von Haeseler, A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.