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Volumn 4, Issue FEB, 2013, Pages

Computer programs and methodologies for the simulation of DNA sequence data with recombination

(1)  Arenas, Miguel a  

a CSIC   (Spain)

Author keywords

DNA sequences; Recombination; Recombination breakpoints; Recombination hotspots; Recombination phylogenetic bias; Simulation

Indexed keywords


EID: 84876070521     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2013.00009     Document Type: Short Survey
Times cited : (11)

References (96)
  • 1
    • 0042208362 scopus 로고    scopus 로고
    • Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    • Anisimova, M., Nielsen, R., and Yang, Z. (2003). Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164, 1229-1236.
    • (2003) Genetics , vol.164 , pp. 1229-1236
    • Anisimova, M.1    Nielsen, R.2    Yang, Z.3
  • 2
    • 84855717407 scopus 로고    scopus 로고
    • Genome-wide heterogeneity of nucleotide substitution model fit
    • Arbiza, L., Patricio, M., Dopazo, H., and Posada, D. (2011). Genome-wide heterogeneity of nucleotide substitution model fit. Genome Biol. Evol. 3, 896-908.
    • (2011) Genome Biol. Evol. , vol.3 , pp. 896-908
    • Arbiza, L.1    Patricio, M.2    Dopazo, H.3    Posada, D.4
  • 3
    • 84863707192 scopus 로고    scopus 로고
    • Simulation of molecular data under diverse evolutionary scenarios
    • doi:10.1371/journal.pcbi.1002495
    • Arenas, M. (2012). Simulation of molecular data under diverse evolutionary scenarios. PLoS Comput. Biol. 8:e1002495. doi:10.1371/journal.pcbi.1002495
    • (2012) PLoS Comput. Biol. , vol.8
    • Arenas, M.1
  • 4
    • 84871831791 scopus 로고    scopus 로고
    • Influence of admixture and paleolithic range contractions on current European diversity gradients
    • Arenas, M., Francois, O., Currat, M., Ray, N., and Excoffier, L. (2013). Influence of admixture and paleolithic range contractions on current European diversity gradients. Mol. Biol. Evol. 30, 57-61.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 57-61
    • Arenas, M.1    Francois, O.2    Currat, M.3    Ray, N.4    Excoffier, L.5
  • 5
    • 77952358764 scopus 로고    scopus 로고
    • Characterization of phylogenetic networks with nettest
    • doi:10.1186/1471-2105-11-268
    • Arenas, M., Patricio, M., Posada, D., and Valiente, G. (2010). Characterization of phylogenetic networks with nettest. BMC Bioinformatics 11:268. doi:10.1186/1471-2105-11-268
    • (2010) BMC Bioinformatics , vol.11 , pp. 268
    • Arenas, M.1    Patricio, M.2    Posada, D.3    Valiente, G.4
  • 6
    • 38349167557 scopus 로고    scopus 로고
    • Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography
    • doi:10.1186/1471-2105-8-458
    • Arenas, M., and Posada, D. (2007). Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 8:458. doi:10.1186/1471-2105-8-458
    • (2007) BMC Bioinformatics , vol.8 , pp. 458
    • Arenas, M.1    Posada, D.2
  • 7
    • 77749261568 scopus 로고    scopus 로고
    • Coalescent simulation of intracodon recombination
    • Arenas, M., and Posada, D. (2010a). Coalescent simulation of intracodon recombination. Genetics 184, 429-437.
    • (2010) Genetics , vol.184 , pp. 429-437
    • Arenas, M.1    Posada, D.2
  • 8
    • 78650893894 scopus 로고    scopus 로고
    • Computational design of centralized HIV-1 genes
    • Arenas, M., and Posada, D. (2010b). Computational design of centralized HIV-1 genes. Curr. HIV Res. 8, 613-621.
    • (2010) Curr. HIV Res. , vol.8 , pp. 613-621
    • Arenas, M.1    Posada, D.2
  • 9
    • 77955885762 scopus 로고    scopus 로고
    • The effect of recombination on the reconstruction of ancestral sequences
    • Arenas, M., and Posada, D. (2010c). The effect of recombination on the reconstruction of ancestral sequences. Genetics 184, 1133-1139.
    • (2010) Genetics , vol.184 , pp. 1133-1139
    • Arenas, M.1    Posada, D.2
  • 10
    • 84938517375 scopus 로고    scopus 로고
    • Simulation of coding sequence evolution
    • eds G. M. Cannarozzi and A. Schneider (Oxford: Oxford University Press)
    • Arenas, M., and Posada, D. (2012). "Simulation of coding sequence evolution," in Codon Evolution, eds G. M. Cannarozzi and A. Schneider (Oxford: Oxford University Press), 126-132.
    • (2012) Codon Evolution , pp. 126-132
    • Arenas, M.1    Posada, D.2
  • 11
    • 84862637315 scopus 로고    scopus 로고
    • Consequences of range contractions and range shifts on molecular diversity
    • Arenas, M., Ray, N., Currat, M., and Excoffier, L. (2012). Consequences of range contractions and range shifts on molecular diversity. Mol. Biol. Evol. 29, 207-218.
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 207-218
    • Arenas, M.1    Ray, N.2    Currat, M.3    Excoffier, L.4
  • 12
    • 56449114514 scopus 로고    scopus 로고
    • Characterization of reticulate networks based on the coalescent with recombination
    • Arenas, M., Valiente, G., and Posada, D. (2008). Characterization of reticulate networks based on the coalescent with recombination. Mol. Biol. Evol. 25, 2517-2520.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 2517-2520
    • Arenas, M.1    Valiente, G.2    Posada, D.3
  • 13
    • 66449104096 scopus 로고    scopus 로고
    • Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach
    • Arenas, M., Villaverde, M. C., and Sussman, F. (2009). Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach. J. Comput. Chem. 30, 1229-1240.
    • (2009) J. Comput. Chem. , vol.30 , pp. 1229-1240
    • Arenas, M.1    Villaverde, M.C.2    Sussman, F.3
  • 14
    • 0037223888 scopus 로고    scopus 로고
    • The evolutionary genomics of pathogen recombination
    • Awadalla, P. (2003). The evolutionary genomics of pathogen recombination. Nat. Rev. Genet. 4, 50-60.
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 50-60
    • Awadalla, P.1
  • 16
    • 78149388939 scopus 로고    scopus 로고
    • Approximate Bayesian computation in evolution and ecology
    • Beaumont, M. A. (2010). Approximate Bayesian computation in evolution and ecology. Annu. Rev. Ecol. Evol. Syst. 41, 379-405.
    • (2010) Annu. Rev. Ecol. Evol. Syst , vol.41 , pp. 379-405
    • Beaumont, M.A.1
  • 17
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont, M. A., Zhang, W., and Balding, D. J. (2002). Approximate Bayesian computation in population genetics. Genetics 162, 2025-2035.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 18
    • 58149231047 scopus 로고    scopus 로고
    • The impact of reticulate evolution on genome phylogeny
    • Beiko, R. G., Doolittle, W. F., and Charlebois, R. L. (2008). The impact of reticulate evolution on genome phylogeny. Syst. Biol. 57, 844-856.
    • (2008) Syst. Biol. , vol.57 , pp. 844-856
    • Beiko, R.G.1    Doolittle, W.F.2    Charlebois, R.L.3
  • 19
    • 77954818882 scopus 로고    scopus 로고
    • Positive selection of HIV host factors and the evolution of lentivirus genes
    • doi:10.1186/1471-2148-10-186
    • Bozek, K., and Lengauer, T. (2010). Positive selection of HIV host factors and the evolution of lentivirus genes. BMC Evol. Biol. 10:186. doi:10.1186/1471-2148-10-186
    • (2010) BMC Evol. Biol. , vol.10 , pp. 186
    • Bozek, K.1    Lengauer, T.2
  • 20
    • 33748693107 scopus 로고    scopus 로고
    • Serial netevolve: a flexible utility for generating seriallysampled sequences along a tree or recombinant network
    • Buendia, P., and Narasimhan, G. (2006). Serial netevolve: a flexible utility for generating seriallysampled sequences along a tree or recombinant network. Bioinformatics 22, 2313-2314.
    • (2006) Bioinformatics , vol.22 , pp. 2313-2314
    • Buendia, P.1    Narasimhan, G.2
  • 21
    • 0035213313 scopus 로고    scopus 로고
    • Haplotype evolution and linkage disequilibrium: a simulation study
    • Calafell,F.,Grigorenko,E.L.,Chikanian, A. A., and Kidd, K. K. (2001). Haplotype evolution and linkage disequilibrium: a simulation study. Hum. Hered. 51, 85-96.
    • (2001) Hum. Hered. , vol.51 , pp. 85-96
    • Calafell, F.1    Grigorenko, E.L.2    Chikanian, A.A.3    Kidd, K.K.4
  • 22
    • 43849112140 scopus 로고    scopus 로고
    • GENOMEPOP: a program to simulate genomes in populations
    • doi:10.1186/1471-2105-9-223
    • Carvajal-Rodriguez, A. (2008). GENOMEPOP: a program to simulate genomes in populations. BMC Bioinformatics 9:223. doi:10.1186/1471-2105-9-223
    • (2008) BMC Bioinformatics , vol.9 , pp. 223
    • Carvajal-Rodriguez, A.1
  • 24
    • 38649110663 scopus 로고    scopus 로고
    • BEAST: Bayesian evolutionary analysis by sampling trees
    • doi:10.1186/1471-2148-7-214
    • Drummond, A. J., and Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214. doi:10.1186/1471-2148-7-214
    • (2007) BMC Evol. Biol. , vol.7 , pp. 214
    • Drummond, A.J.1    Rambaut, A.2
  • 25
    • 44949198268 scopus 로고    scopus 로고
    • The impact of recombination on nucleotide substitutions in the human genome
    • doi:10.1371/journal.pgen.1000071
    • Duret, L., and Arndt, P. F. (2008). The impact of recombination on nucleotide substitutions in the human genome. PLoS Genet. 4:e1000071. doi:10.1371/journal.pgen.1000071
    • (2008) PLoS Genet , vol.4
    • Duret, L.1    Arndt, P.F.2
  • 27
    • 77955381733 scopus 로고    scopus 로고
    • MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus
    • Ewing, G., and Hermisson, J. (2010). MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26, 2064-2065.
    • (2010) Bioinformatics , vol.26 , pp. 2064-2065
    • Ewing, G.1    Hermisson, J.2
  • 28
    • 79954469204 scopus 로고    scopus 로고
    • Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
    • Excoffier, L., and Foll, M. (2011). Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27, 1332-1334.
    • (2011) Bioinformatics , vol.27 , pp. 1332-1334
    • Excoffier, L.1    Foll, M.2
  • 29
    • 0035793056 scopus 로고    scopus 로고
    • Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
    • Feil, E. J., Holmes, E. C., Bessen, D. E., Chan, M.-S., Day, N. P. J., Enright, M. C., et al. (2001). Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl. Acad. Sci. U.S.A. 98, 182-187.
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 182-187
    • Feil, E.J.1    Holmes, E.C.2    Bessen, D.E.3    Chan, M.-S.4    Day, N.P.J.5    Enright, M.C.6
  • 30
    • 67749108209 scopus 로고    scopus 로고
    • INDELible: a flexible simulator of biological sequence evolution
    • Fletcher, W., and Yang, Z. (2009). INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26, 1879-1888.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 1879-1888
    • Fletcher, W.1    Yang, Z.2
  • 31
    • 33846625056 scopus 로고    scopus 로고
    • Recombination and the nature of bacterial speciation
    • Fraser, C., Hanage, W. P., and Spratt, B. G. (2007). Recombination and the nature of bacterial speciation. Science 315, 476-480.
    • (2007) Science , vol.315 , pp. 476-480
    • Fraser, C.1    Hanage, W.P.2    Spratt, B.G.3
  • 33
    • 33845768012 scopus 로고    scopus 로고
    • Recombination: an underappreciated factor in the evolution of plant genomes
    • Gaut, B. S., Wright, S. I., Rizzon, C., Dvorak, J., and Anderson, L. K. (2007). Recombination: an underappreciated factor in the evolution of plant genomes. Nat. Rev. Genet. 8, 77-84.
    • (2007) Nat. Rev. Genet. , vol.8 , pp. 77-84
    • Gaut, B.S.1    Wright, S.I.2    Rizzon, C.3    Dvorak, J.4    Anderson, L.K.5
  • 34
    • 83455238341 scopus 로고    scopus 로고
    • Biophysical and structural considerations for protein sequence evolution
    • doi:10.1186/1471-2148-11-361
    • Grahnen, J. A., Nandakumar, P., Kubelka, J., and Liberles, D. A. (2011). Biophysical and structural considerations for protein sequence evolution. BMC Evol. Biol. 11:361. doi:10.1186/1471-2148-11-361
    • (2011) BMC Evol. Biol. , vol.11 , pp. 361
    • Grahnen, J.A.1    Nandakumar, P.2    Kubelka, J.3    Liberles, D.A.4
  • 36
    • 0000557367 scopus 로고    scopus 로고
    • An ancestral recombination graph
    • eds P. Donelly and S. Tavaré (Berlin: Springer-Verlag)
    • Griffiths, R. C., and Marjoram, P. (1997). "An ancestral recombination graph," in Progress in Population Genetics and Human Evolution, eds P. Donelly and S. Tavaré (Berlin: Springer-Verlag), 257-270.
    • (1997) Progress in Population Genetics and Human Evolution , pp. 257-270
    • Griffiths, R.C.1    Marjoram, P.2
  • 37
    • 77957934032 scopus 로고    scopus 로고
    • Intragenic recombination as a mechanism of genetic diversity in bluetongue virus
    • He, C. Q., Ding, N. Z., He, M., Li, S. N., Wang, X. M., He, H. B., et al. (2010). Intragenic recombination as a mechanism of genetic diversity in bluetongue virus. J. Virol. 84, 11487-11495.
    • (2010) J. Virol. , vol.84 , pp. 11487-11495
    • He, C.Q.1    Ding, N.Z.2    He, M.3    Li, S.N.4    Wang, X.M.5    He, H.B.6
  • 38
    • 33847273741 scopus 로고    scopus 로고
    • msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
    • Hellenthal, G., and Stephens, M. (2007). msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 23, 520-521.
    • (2007) Bioinformatics , vol.23 , pp. 520-521
    • Hellenthal, G.1    Stephens, M.2
  • 39
    • 56649111423 scopus 로고    scopus 로고
    • A flexible forward simulator for populations subject to selection and demography
    • Hernandez, R. D. (2008). A flexible forward simulator for populations subject to selection and demography. Bioinformatics 24, 2786-2787.
    • (2008) Bioinformatics , vol.24 , pp. 2786-2787
    • Hernandez, R.D.1
  • 40
    • 84855963371 scopus 로고    scopus 로고
    • Computer simulations: tools for population and evolutionary genetics
    • Hoban, S., Bertorelle, G., and Gaggiotti, O. E. (2012). Computer simulations: tools for population and evolutionary genetics. Nat. Rev. Genet. 13, 110-122.
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 110-122
    • Hoban, S.1    Bertorelle, G.2    Gaggiotti, O.E.3
  • 41
    • 0020744702 scopus 로고
    • Properties of a neutral allele model with intragenic recombination
    • Hudson, R. R. (1983). Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23, 183-201.
    • (1983) Theor. Popul. Biol. , vol.23 , pp. 183-201
    • Hudson, R.R.1
  • 42
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson, R. R. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 43
    • 0031678692 scopus 로고    scopus 로고
    • Splitstree: analyzing and visualizing evolutionary data
    • Huson, D. H. (1998). Splitstree: analyzing and visualizing evolutionary data. Bioinformatics 14, 68-73.
    • (1998) Bioinformatics , vol.14 , pp. 68-73
    • Huson, D.H.1
  • 44
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson, D. H., and Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254-267.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 45
    • 17744395033 scopus 로고    scopus 로고
    • Datamonkey:rapid detection of selective pressure on individual sites of codon alignments
    • Kosakovsky Pond, S. L., and Frost, S. D. (2005). Datamonkey:rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 21, 2531-2533.
    • (2005) Bioinformatics , vol.21 , pp. 2531-2533
    • Kosakovsky Pond, S.L.1    Frost, S.D.2
  • 48
    • 58149168840 scopus 로고    scopus 로고
    • The population genetics of dN/dS
    • doi:10.1371/journal.pgen.1000304
    • Kryazhimskiy, S., and Plotkin, J. B. (2008). The population genetics of dN/dS. PLoS Genet. 4:e1000304. doi:10.1371/journal.pgen.1000304
    • (2008) PLoS Genet , vol.4
    • Kryazhimskiy, S.1    Plotkin, J.B.2
  • 49
    • 7244221627 scopus 로고    scopus 로고
    • SIMCOAL 2,0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
    • Laval, G., and Excoffier, L. (2004). SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics 20, 2485-2487.
    • (2004) Bioinformatics , vol.20 , pp. 2485-2487
    • Laval, G.1    Excoffier, L.2
  • 50
    • 34547830810 scopus 로고    scopus 로고
    • GENOME: a rapid coalescent-based whole genome simulator
    • Liang, L., Zollner, S., and Abecasis, G. R. (2007). GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 23, 1565-1567.
    • (2007) Bioinformatics , vol.23 , pp. 1565-1567
    • Liang, L.1    Zollner, S.2    Abecasis, G.R.3
  • 51
    • 63449126121 scopus 로고    scopus 로고
    • A survey of genetic simulation software for population and epidemiological studies
    • Liu, Y., Athanasiadis, G., and Weale, M. E. (2008). A survey of genetic simulation software for population and epidemiological studies. Hum. Genomics 3, 79-86.
    • (2008) Hum. Genomics , vol.3 , pp. 79-86
    • Liu, Y.1    Athanasiadis, G.2    Weale, M.E.3
  • 52
    • 18744408450 scopus 로고    scopus 로고
    • Role of recombination in evolution of enteroviruses
    • Lukashev, A. N. (2005). Role of recombination in evolution of enteroviruses. Rev. Med. Virol. 15, 157-167.
    • (2005) Rev. Med. Virol. , vol.15 , pp. 157-167
    • Lukashev, A.N.1
  • 53
    • 80054087236 scopus 로고    scopus 로고
    • Analysing recombination in nucleotide sequences
    • Martin, D. P., Lemey, P., and Posada, D. (2011). Analysing recombination in nucleotide sequences. Mol. Ecol. Resour. 11, 943-955.
    • (2011) Mol. Ecol. Resour. , vol.11 , pp. 943-955
    • Martin, D.P.1    Lemey, P.2    Posada, D.3
  • 55
    • 67649171544 scopus 로고    scopus 로고
    • Tracing the evolution of competence in Haemophilus influenzae
    • doi:10.1371/journal.pone.0005854
    • Maughan, H., and Redfield, R. J. (2009). Tracing the evolution of competence in Haemophilus influenzae. PLoS ONE 4:e5854. doi:10.1371/journal.pone.0005854
    • (2009) PLoS ONE , vol.4
    • Maughan, H.1    Redfield, R.J.2
  • 57
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • Metzker, M. L. (2010). Sequencing technologies - the next generation. Nat. Rev. Genet. 11, 31-46.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 31-46
    • Metzker, M.L.1
  • 58
    • 84882454218 scopus 로고    scopus 로고
    • Coalescent theory
    • 3rd Edn, eds D. J. Balding, M. Bishop, and C. Cannings (Chichester: JohnWiley & Sons Ltd)
    • Nordborg, M. (2007). "Coalescent theory," in Handbook of Statistical Genetics, 3rd Edn, eds D. J. Balding, M. Bishop, and C. Cannings (Chichester: JohnWiley & Sons Ltd), 843-877.
    • (2007) Handbook of Statistical Genetics , pp. 843-877
    • Nordborg, M.1
  • 59
    • 77957728670 scopus 로고    scopus 로고
    • On optimal selection of summary statistics for approximate Bayesian computation
    • Nunes, M. A., and Balding, D. J. (2010). On optimal selection of summary statistics for approximate Bayesian computation. Stat. Appl. Genet. Mol. Biol. 9, 34.
    • (2010) Stat. Appl. Genet. Mol. Biol. , vol.9 , pp. 34
    • Nunes, M.A.1    Balding, D.J.2
  • 60
    • 45849134174 scopus 로고    scopus 로고
    • Exploring population genetic models with recombination using efficient forward-time simulations
    • Padhukasahasram, B., Marjoram, P., Wall, J. D., Bustamante, C. D., and Nordborg, M. (2008). Exploring population genetic models with recombination using efficient forward-time simulations. Genetics 178, 2417-2427.
    • (2008) Genetics , vol.178 , pp. 2417-2427
    • Padhukasahasram, B.1    Marjoram, P.2    Wall, J.D.3    Bustamante, C.D.4    Nordborg, M.5
  • 61
    • 4544330271 scopus 로고    scopus 로고
    • Simulation as experiment: a philosophical reassessment for biological modeling
    • Peck, S. L. (2004). Simulation as experiment: a philosophical reassessment for biological modeling. Trends Ecol. Evol. (Amst.) 19, 530-534.
    • (2004) Trends Ecol. Evol. (Amst. ) , vol.19 , pp. 530-534
    • Peck, S.L.1
  • 62
    • 34047228125 scopus 로고    scopus 로고
    • Forward-time simulations of human populations with complex diseases
    • doi:10.1371/journal.pgen.0030047
    • Peng, B., Amos, C. I., and Kimmel, M. (2007). Forward-time simulations of human populations with complex diseases. PLoS Genet. 3:e47. doi:10.1371/journal.pgen.0030047
    • (2007) PLoS Genet , vol.3
    • Peng, B.1    Amos, C.I.2    Kimmel, M.3
  • 63
    • 24644505748 scopus 로고    scopus 로고
    • Simupop: a forward-time population genetics simulation environment
    • Peng, B., and Kimmel, M. (2005). Simupop: a forward-time population genetics simulation environment. Bioinformatics 21, 3686-3687.
    • (2005) Bioinformatics , vol.21 , pp. 3686-3687
    • Peng, B.1    Kimmel, M.2
  • 64
    • 79952527522 scopus 로고    scopus 로고
    • Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand
    • doi:10.1371/journal.pone.0016902
    • Perez-Losada, M., Jobes, D. V., Sinangil, F., Crandall, K. A., Arenas, M., Posada, D., et al. (2011). Phylodynamics of HIV-1 from a phase III AIDS vaccine trial in Bangkok, Thailand. PLoS ONE 6:e16902. doi:10.1371/journal.pone.0016902
    • (2011) PLoS ONE , vol.6
    • Perez-Losada, M.1    Jobes, D.V.2    Sinangil, F.3    Crandall, K.A.4    Arenas, M.5    Posada, D.6
  • 66
    • 79959575355 scopus 로고    scopus 로고
    • Mutation rate switch inside Eurasian mitochondrial haplogroups: impact of selection and consequences for dating settlement in Europe
    • doi:10.1371/journal.pone.0021543
    • Pierron, D., Chang, I., Arachiche, A., Heiske, M., Thomas, O., Borlin, M., et al. (2011). Mutation rate switch inside Eurasian mitochondrial haplogroups: impact of selection and consequences for dating settlement in Europe. PLoS ONE 6:e21543. doi:10.1371/journal.pone.0021543
    • (2011) PLoS ONE , vol.6
    • Pierron, D.1    Chang, I.2    Arachiche, A.3    Heiske, M.4    Thomas, O.5    Borlin, M.6
  • 67
    • 0034814736 scopus 로고    scopus 로고
    • Unveiling the molecular clock in the presence of recombination
    • Posada, D. (2001). Unveiling the molecular clock in the presence of recombination. Mol. Biol. Evol. 18, 1976-1978.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1976-1978
    • Posada, D.1
  • 68
    • 0035923699 scopus 로고    scopus 로고
    • Evaluation of methods for detecting recombination from DNA sequences: computer simulations
    • Posada, D., and Crandall, K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. U.S.A. 98, 13757-13762.
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 13757-13762
    • Posada, D.1    Crandall, K.A.2
  • 69
    • 0036183042 scopus 로고    scopus 로고
    • The effect of recombination on the accuracy of phylogeny estimation
    • Posada, D., and Crandall, K. A. (2002). The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54, 396-402.
    • (2002) J. Mol. Evol. , vol.54 , pp. 396-402
    • Posada, D.1    Crandall, K.A.2
  • 71
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: an application for the Monte carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., and Grassly, N. C. (1997). Seq-gen: an application for the Monte carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13, 235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 73
    • 78449304078 scopus 로고    scopus 로고
    • SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination
    • Ray, N., Currat, M., Foll, M., and Excoffier, L. (2010). SPLATCHE2: a spatially explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics 26, 2993-2994.
    • (2010) Bioinformatics , vol.26 , pp. 2993-2994
    • Ray, N.1    Currat, M.2    Foll, M.3    Excoffier, L.4
  • 76
    • 27544497650 scopus 로고    scopus 로고
    • Calibrating a coalescent simulation of human genome sequence variation
    • Schaffner, S. F., Foo, C., Gabriel, S., Reich, D., Daly, M. J., and Altshuler, D. (2005). Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 15, 1576-1583.
    • (2005) Genome Res , vol.15 , pp. 1576-1583
    • Schaffner, S.F.1    Foo, C.2    Gabriel, S.3    Reich, D.4    Daly, M.J.5    Altshuler, D.6
  • 77
    • 0033793521 scopus 로고    scopus 로고
    • Consequences of recombination on traditional phylogenetic analysis
    • Schierup, M. H., and Hein, J. (2000a). Consequences of recombination on traditional phylogenetic analysis. Genetics 156, 879-891.
    • (2000) Genetics , vol.156 , pp. 879-891
    • Schierup, M.H.1    Hein, J.2
  • 78
    • 0033805038 scopus 로고    scopus 로고
    • Recombination and the molecular clock
    • Schierup, M. H., and Hein, J. (2000b). Recombination and the molecular clock. Mol. Biol. Evol. 17, 1578-1579.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1578-1579
    • Schierup, M.H.1    Hein, J.2
  • 79
    • 84865078007 scopus 로고    scopus 로고
    • Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach
    • Sohn, K. A., Ghahramani, Z., and Xing, E. P. (2012). Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach. Genetics 191, 1295-1308.
    • (2012) Genetics , vol.191 , pp. 1295-1308
    • Sohn, K.A.1    Ghahramani, Z.2    Xing, E.P.3
  • 80
    • 33749416027 scopus 로고    scopus 로고
    • The influence of recombination on human genetic diversity
    • doi:10.1371/journal.pgen.0020148
    • Spencer, C. C., Deloukas, P., Hunt, S., Mullikin, J., Myers, S., Silverman, B., et al. (2006). The influence of recombination on human genetic diversity. PLoS Genet. 2:e148. doi:10.1371/journal.pgen.0020148
    • (2006) PLoS Genet , vol.2
    • Spencer, C.C.1    Deloukas, P.2    Hunt, S.3    Mullikin, J.4    Myers, S.5    Silverman, B.6
  • 81
    • 73349096292 scopus 로고    scopus 로고
    • Biological sequence simulation for testing complex evolutionary hypotheses: indel-seq-gen version 2.0
    • Strope, C. L., Abel, K., Scott, S. D., and Moriyama, E. N. (2009). Biological sequence simulation for testing complex evolutionary hypotheses: indel-seq-gen version 2.0. Mol. Biol. Evol. 26, 2581-2593.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 2581-2593
    • Strope, C.L.1    Abel, K.2    Scott, S.D.3    Moriyama, E.N.4
  • 82
    • 80052155692 scopus 로고    scopus 로고
    • "Patchy-tachy" leads to false positives for recombination
    • Sun, S., Evans, B. J., and Golding, G. B. (2011). "Patchy-tachy" leads to false positives for recombination. Mol. Biol. Evol. 28, 2549-2559.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2549-2559
    • Sun, S.1    Evans, B.J.2    Golding, G.B.3
  • 83
    • 67650895090 scopus 로고    scopus 로고
    • Mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection
    • doi:10.1186/1471-2105-10-166
    • Teshima, K. M., and Innan, H. (2009). Mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. BMC Bioinformatics 10:166. doi:10.1186/1471-2105-10-166
    • (2009) BMC Bioinformatics , vol.10 , pp. 166
    • Teshima, K.M.1    Innan, H.2
  • 86
    • 63549098393 scopus 로고    scopus 로고
    • Accurate detection of recombinant breakpoints in whole-genome alignments
    • doi:10.1371/journal. pcbi.1000318
    • Westesson, O., and Holmes, I. (2009). Accurate detection of recombinant breakpoints in whole-genome alignments. PLoS Comput. Biol. 5:e1000318. doi:10.1371/journal. pcbi.1000318
    • (2009) PLoS Comput. Biol. , vol.5
    • Westesson, O.1    Holmes, I.2
  • 87
    • 58449131619 scopus 로고    scopus 로고
    • Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni
    • Wilson,D. J.,Gabriel,E.,Leatherbarrow, A. J.,Cheesbrough,J.,Gee,S.,Bolton, E., et al. (2009). Rapid evolution and the importance of recombination to the gastroenteric pathogen Campylobacter jejuni. Mol. Biol. Evol. 26, 385-397.
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 385-397
    • Wilson, D.J.1    Gabriel, E.2    Leatherbarrow, A.J.3    Cheesbrough, J.4    Gee, S.5    Bolton, E.6
  • 88
    • 0034815265 scopus 로고    scopus 로고
    • A simulation study of the reliability of recombination detection methods
    • Wiuf, C., Christensen, T., and Hein, J. (2001). A simulation study of the reliability of recombination detection methods. Mol. Biol. Evol. 18, 1929-1939.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1929-1939
    • Wiuf, C.1    Christensen, T.2    Hein, J.3
  • 89
    • 0038530758 scopus 로고    scopus 로고
    • A coalescent model of recombination hotspots
    • Wiuf, C., and Posada, D. (2003). A coalescent model of recombination hotspots. Genetics 164, 407-417.
    • (2003) Genetics , vol.164 , pp. 407-417
    • Wiuf, C.1    Posada, D.2
  • 90
    • 44849122679 scopus 로고    scopus 로고
    • A comparison of phylogenetic network methods using computer simulation
    • doi:10.1371/journal.pone.0001913
    • Woolley, S. M., Posada, D., and Crandall, K. A. (2008). A comparison of phylogenetic network methods using computer simulation. PLoS ONE 3:e1913. doi:10.1371/journal.pone.0001913
    • (2008) PLoS ONE , vol.3
    • Woolley, S.M.1    Posada, D.2    Crandall, K.A.3
  • 91
    • 0032853634 scopus 로고    scopus 로고
    • Evolutionary aspects of recombination in RNA viruses
    • Worobey, M., and Holmes, E. C. (1999). Evolutionary aspects of recombination in RNA viruses. J. Gen. Virol. 80, 2535-2543.
    • (1999) J. Gen. Virol. , vol.80 , pp. 2535-2543
    • Worobey, M.1    Holmes, E.C.2
  • 92
    • 0030683599 scopus 로고    scopus 로고
    • PAML: a program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. (1997). PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555-556.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1
  • 94
    • 0034097381 scopus 로고    scopus 로고
    • Codonsubstitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., Nielsen, R., Goldman, N., and Pedersen, A.-M. K. (2000). Codonsubstitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.-M.4
  • 96
    • 0036827628 scopus 로고    scopus 로고
    • Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots
    • Zhuang, J., Jetzt, A. E., Sun, G., Yu, H., Klarmann, G., Ron, Y., et al. (2002). Human immunodeficiency virus type 1 recombination: rate, fidelity, and putative hot spots. J. Virol. 76, 11273-11282.
    • (2002) J. Virol. , vol.76 , pp. 11273-11282
    • Zhuang, J.1    Jetzt, A.E.2    Sun, G.3    Yu, H.4    Klarmann, G.5    Ron, Y.6


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