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Volumn 64, Issue 1, 2015, Pages e42-e62

The inference of gene trees with species trees

Author keywords

Algorithm; amalgamation; Bayesian inference; birth death model; coalescent; dynamic programming; gene duplication; gene loss; gene transfer; gene tree; hybridization; maximum likelihood; phylogenetics; species tree

Indexed keywords

BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETICS; GENOME; MUTATION; PHYLOGENY; SPECIES DIFFERENTIATION;

EID: 84928749156     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syu048     Document Type: Article
Times cited : (187)

References (142)
  • 2
  • 3
    • 65249107239 scopus 로고    scopus 로고
    • Simultaneous Bayesian gene tree reconstruction and reconciliation analysis
    • Akerborg O., Sennblad B., Arvestad L., Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc. Nat. Acad. Sci. 106:5714-5719
    • (2009) Proc. Nat. Acad. Sci , vol.106 , pp. 5714-5719
    • Akerborg, O.1    Sennblad, B.2    Arvestad, L.3    Lagergren, J.4
  • 4
    • 82655183796 scopus 로고    scopus 로고
    • Nonmonophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically Densely sampled dataset
    • Alstr P., Hna S., Gelang M., Ericson P. G. P., Olsson U. 2011. Nonmonophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically Densely sampled dataset. BMC Evol. Biol. 11:352
    • (2011) BMC Evol. Biol , vol.11 , pp. 352
    • Alstr, P.1    Hna, S.2    Gelang, M.3    Ericson, P.G.P.4    Olsson, U.5
  • 5
    • 79960041437 scopus 로고    scopus 로고
    • Detecting phylogenetic breakpoints and discordance from genome-wiDe alignments for species tree reconstruction
    • Ana C. 2011. Detecting phylogenetic breakpoints and discordance from genome-wiDe alignments for species tree reconstruction. Genome Biol. Evol. 3:246-258
    • (2011) Genome Biol. Evol , vol.3 , pp. 246-258
    • Ana, C.1
  • 7
    • 2342651581 scopus 로고    scopus 로고
    • Bayesian gene/species tree reconciliation and orthology analysis using MCMC
    • Arvestad L. 2003. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19:7i-15
    • (2003) Bioinformatics , vol.19 , pp. 71-15
    • Arvestad, L.1
  • 9
    • 84874708873 scopus 로고    scopus 로고
    • Systematic inference of highways of horizontal gene transfer in prokaryotes
    • Bansal M. S., Banay G., Harlow T. J., Gogarten J. P., Shamir R. 2013. Systematic inference of highways of horizontal gene transfer in prokaryotes. Bioinformatics 29:571-579
    • (2013) Bioinformatics , vol.29 , pp. 571-579
    • Bansal, M.S.1    Banay, G.2    Harlow, T.J.3    Gogarten, J.P.4    Shamir, R.5
  • 10
    • 75149135738 scopus 로고    scopus 로고
    • Efficient genomescale phylogenetic analysis under the duplication-loss and Deep coalescence cost moDels
    • Bansal M. S., Burleigh J. G., Eulenstein O. 2010. Efficient genomescale phylogenetic analysis unDer the duplication-loss and Deep coalescence cost moDels. BMC Bioinformatics. 13:S11
    • (2010) BMC Bioinformatics , vol.13 , pp. S11
    • Bansal, M.S.1    Burleigh, J.G.2    Eulenstein, O.3
  • 11
    • 84888134002 scopus 로고    scopus 로고
    • Inferring optimal species trees under duplication and loss. Proceedings
    • Bayzid M. S., Mirarab S., Warnow T. 2013. Inferring optimal species trees unDer duplication and loss. Proceedings, Pacific Symposium on Biocomputing, vol. 18, p. 250-261
    • (2013) Pacific Symposium on Biocomputing , vol.18 , pp. 250-261
    • Bayzid, M.S.1    Mirarab, S.2    Warnow, T.3
  • 12
    • 33645568886 scopus 로고    scopus 로고
    • Phylogenetic iDentification of lateral genetic transfer events
    • Beiko R. G., Hamilton N. 2006. Phylogenetic iDentification of lateral genetic transfer events. BMC Evol. Biol. 6:15
    • (2006) BMC Evol. Biol , vol.6 , pp. 15
    • Beiko, R.G.1    Hamilton, N.2
  • 14
    • 72049128651 scopus 로고    scopus 로고
    • Unifying vertical and nonvertical evolution: A stochasticARG-based framework
    • Bloomquist E. W., Suchard M. A. 2010. Unifying vertical and nonvertical evolution: a stochasticARG-based framework. Syst. Biol. 59:27-41
    • (2010) Syst. Biol , vol.59 , pp. 27-41
    • Bloomquist, E.W.1    Suchard, M.A.2
  • 15
    • 77949616292 scopus 로고    scopus 로고
    • Genomes as documents of evolutionary history
    • Boussau B., Daubin V. 2010. Genomes as documents of evolutionary history. Trends Ecol. Evol. 25:224-232
    • (2010) Trends Ecol. Evol , vol.25 , pp. 224-232
    • Boussau, B.1    Daubin, V.2
  • 16
    • 35248857403 scopus 로고    scopus 로고
    • Efficient likelihood computations with nonreversible moDels of evolution
    • Boussau B., Gouy M. 2006. Efficient likelihood computations with nonreversible moDels of evolution. Syst. Biol. 55:756-768
    • (2006) Syst. Biol , vol.55 , pp. 756-768
    • Boussau, B.1    Gouy, M.2
  • 17
    • 68149165460 scopus 로고    scopus 로고
    • AmixturemoDel and a hidDen markov moDel to simultaneously Detect recombination breakpoints and reconstruct phylogenies
    • Boussau B., Guuen L., Gouy M. 2009. AmixturemoDel and a hidDen markov moDel to simultaneously Detect recombination breakpoints and reconstruct phylogenies. Evol. Bioinformatics 5:67-79
    • (2009) Evol. Bioinformatics , vol.5 , pp. 67-79
    • Boussau, B.1    Guuen, L.2    Gouy, M.3
  • 19
    • 70349464621 scopus 로고    scopus 로고
    • An epistatic ratchet constrains the direction of glucocorticoid receptor evolution
    • Bridgham J. T., Ortlund E. A., Thornton J. W. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519
    • (2009) Nature , vol.461 , pp. 515-519
    • Bridgham, J.T.1    Ortlund, E.A.2    Thornton, J.W.3
  • 20
    • 84864697376 scopus 로고    scopus 로고
    • Inferring species trees directly from biallelic genetic markers: Bypassing gene trees in a full coalescent analysis
    • Bryant D., Bouckaert R., Felsenstein J., Rosenberg N. A., RoyChoudhury A. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 29:1917-1932
    • (2012) Mol. Biol. Evol , vol.29 , pp. 1917-1932
    • Bryant, D.1    Bouckaert, R.2    Felsenstein, J.3    Rosenberg, N.A.4    Roychoudhury, A.5
  • 21
  • 25
    • 84877145695 scopus 로고    scopus 로고
    • Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and Deep coalescence
    • Chaudhary R., Burleigh J. G., Eulenstein O. 2012. Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and Deep coalescence. BMC Bioinformatics 13:S11
    • (2012) BMC Bioinformatics , vol.13 , pp. S11
    • Chaudhary, R.1    Burleigh, J.G.2    Eulenstein, O.3
  • 26
    • 1642274782 scopus 로고    scopus 로고
    • Gene tree parsimony vs uninoDe coding for phylogenetic reconstruction
    • Cotton J. A., Page R. D. M. 2003. Gene tree parsimony vs uninoDe coding for phylogenetic reconstruction. Mol. Phylogenet. Evol. 29:298-308
    • (2003) Mol. Phylogenet. Evol , vol.29 , pp. 298-308
    • Cotton, J.A.1    Page, R.D.M.2
  • 27
    • 33745796718 scopus 로고    scopus 로고
    • A probabilistic moDel for gene content evolution with duplication, loss, and horizontal transfer
    • Csuros M., Miklos I., Csur M., Mikl I. 2006. A probabilistic moDel for gene content evolution with duplication, loss, and horizontal transfer. Res. Comput. Mol. Biol. q-bio. PE:206-220
    • (2006) Res. Comput. Mol. Biol. Q-bio. PE , pp. 206-220
    • Csuros, M.1    Miklos, I.2    Csur, M.3    Mikl, I.4
  • 28
    • 48249144818 scopus 로고    scopus 로고
    • Dynamics of genome rearrangement in bacterial populations
    • Darling A. E., Mikl I., Ragan M. A. 2008. Dynamics of genome rearrangement in bacterial populations. PLoS Genet. 4:e1000128
    • (2008) PLoS Genet , vol.4 , pp. e1000128
    • Darling, A.E.1    Mikl, I.2    Ragan, M.A.3
  • 29
    • 78650987950 scopus 로고    scopus 로고
    • Rapid evolutionary innovation during an archaean genetic expansion
    • David L. A., Alm E. J. 2011. Rapid evolutionary innovation during an archaean genetic expansion. Nature 469:93-96
    • (2011) Nature , vol.469 , pp. 93-96
    • David, L.A.1    Alm, E.J.2
  • 30
    • 84888597013 scopus 로고    scopus 로고
    • Linking great Apes genome evolution across time scales using polymorphism-Aware phylogenetic moDels
    • De Maio N., Schlterer C., Kosiol C. 2013. Linking great Apes genome evolution across time scales using polymorphism-Aware phylogenetic moDels. Mol. Biol. Evol. 30:2249-2262
    • (2013) Mol. Biol. Evol , vol.30 , pp. 2249-2262
    • De Maio, N.1    Schlterer, C.2    Kosiol, C.3
  • 31
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan J. H., Rosenberg N. A. 2006. Discordance of species trees with their most likely gene trees. PLoS Genet. 2:e68
    • (2006) PLoS Genet , vol.2 , pp. e68
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 32
    • 13244292527 scopus 로고    scopus 로고
    • Gene tree distributions under the coalescent process
    • Degnan J. H., Salter L. A. 2005. Gene tree distributions unDer the coalescent process. Evol. 59:24-37
    • (2005) Evol , vol.59 , pp. 24-37
    • Degnan, J.H.1    Salter, L.A.2
  • 33
    • 79251573854 scopus 로고    scopus 로고
    • Inference of homologous recombination in bacteria using whole-genome sequences
    • DiDelot X., Lawson D., Darling A., Falush D. 2010. Inference of homologous recombination in bacteria using whole-genome sequences. Genet. 186:1435-1449
    • (2010) Genet , vol.186 , pp. 1435-1449
    • Didelot, X.1    Lawson, D.2    Darling, A.3    Falush, D.4
  • 34
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • New York, NY
    • Doolittle W. F. 1999. Phylogenetic classification and the universal tree. Science (New York, NY) 284:2124-2129
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 36
    • 80053210637 scopus 로고    scopus 로고
    • MoDels, algorithms and programs for phylogeny reconciliation
    • Doyon J.-P., Ranwez V., Daubin V., Berry V. 2011. MoDels, algorithms and programs for phylogeny reconciliation. Brief. Bioinform. 12:392-400
    • (2011) Brief. Bioinform , vol.12 , pp. 392-400
    • Doyon, J.-P.1    Ranwez, V.2    Daubin, V.3    Berry, V.4
  • 37
    • 84864530626 scopus 로고    scopus 로고
    • Bayesian phylogenetics with beauti and the beast 1. 7
    • Drummond A. J., Suchard M. A., Xie D., Rambaut A. 2012. Bayesian phylogenetics with beauti and the beast 1. 7. Mol. Biol. Evol. 29:1969-1973
    • (2012) Mol. Biol. Evol , vol.29 , pp. 1969-1973
    • Drummond, A.J.1    Suchard, M.A.2    Xie, D.3    Rambaut, A.4
  • 40
    • 34347256397 scopus 로고    scopus 로고
    • High-resolution species trees without concatenation
    • Edwards S. V., Liu L., Pearl D. K. 2007. High-resolution species trees without concatenation. Proc. Nat. Acad. Sci. USA. 104:5936-5941
    • (2007) Proc. Nat. Acad. Sci. USA , vol.104 , pp. 5936-5941
    • Edwards, S.V.1    Liu, L.2    Pearl, D.K.3
  • 41
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376
    • (1981) J. Mol. Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 42
    • 0024152983 scopus 로고
    • Phylogenies from molecular sequences: Inference and reliability
    • Felsenstein J. 1988. Phylogenies from molecular sequences: inference and reliability. Annu. Rev. Genet. 22:521-565
    • (1988) Annu. Rev. Genet , vol.22 , pp. 521-565
    • Felsenstein, J.1
  • 46
    • 67651064681 scopus 로고    scopus 로고
    • Horizontal gene transfer from extinct and extant lineages: Biological innovation and the coral of life
    • Fournier G. P., Huang J., Gogarten J. P. 2009. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos. Trans. R. Soc. Lond. B Biol. Sci. 364:2229-2239
    • (2009) Philos. Trans. R. Soc. Lond. B Biol. Sci , vol.364 , pp. 2229-2239
    • Fournier, G.P.1    Huang, J.2    Gogarten, J.P.3
  • 47
    • 38449096427 scopus 로고    scopus 로고
    • A moDel of horizontal gene transfer and the bacterial phylogeny problem
    • Galtier N. 2007. A moDel of horizontal gene transfer and the bacterial phylogeny problem. Syst. Biol. 56:633-642
    • (2007) Syst. Biol , vol.56 , pp. 633-642
    • Galtier, N.1
  • 48
    • 38949093003 scopus 로고    scopus 로고
    • Palaeotemperature trend for Precambrian life inferred from resurrected proteins
    • Gaucher E. A., Govindarajan S., Ganesh O. K. 2008. Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451:704-707
    • (2008) Nature , vol.451 , pp. 704-707
    • Gaucher, E.A.1    Govindarajan, S.2    Ganesh, O.K.3
  • 49
    • 0141828152 scopus 로고    scopus 로고
    • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    • Gaucher E. A., Thomson J. M., Burgan M. F., Benner S. A. 2003. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425:285-288
    • (2003) Nature , vol.425 , pp. 285-288
    • Gaucher, E.A.1    Thomson, J.M.2    Burgan, M.F.3    Benner, S.A.4
  • 50
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • Goodman M., Czelusniak J., Moore G. W., Romero-Herrera A. E., Matsuda G. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28:132-163
    • (1979) Syst. Zool , vol.28 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 51
    • 84857090152 scopus 로고    scopus 로고
    • Maximum likelihood moDels and algorithms for gene tree evolution with duplications and losses
    • Gecki P., Burleigh G. J., Eulenstein O. 2011. Maximum likelihood moDels and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics 12:S15
    • (2011) BMC Bioinformatics , vol.12 , pp. S15
    • Gecki, P.1    Burleigh, G.J.2    Eulenstein, O.3
  • 52
    • 84891589817 scopus 로고    scopus 로고
    • Drml: Probabilistic moDeling of gene duplications
    • Gecki P., Eulenstein O. 2013. Drml: probabilistic moDeling of gene duplications. J. Comput. Biol. 21:89-98
    • (2013) J. Comput. Biol , vol.21 , pp. 89-98
    • Gecki, P.1    Eulenstein, O.2
  • 53
    • 79955416536 scopus 로고    scopus 로고
    • Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wiDe data within a Bayesian framework
    • Gray R. R., Tatem A. J., Johnson J. A., Alekseyenko A. V., Pybus O. G., Suchard M. A., Salemi M. 2011. Testing spatiotemporal hypothesis of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wiDe data within a Bayesian framework. Mol. Biol. Evol. 28:1593-603
    • (2011) Mol. Biol. Evol , vol.28 , pp. 1593-1603
    • Gray, R.R.1    Tatem, A.J.2    Johnson, J.A.3    Alekseyenko, A.V.4    Pybus, O.G.5    Suchard, M.A.6    Salemi, M.7
  • 54
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon S., Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704
    • (2003) Syst. Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 55
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3. 0
    • Guindon S., Dufayard J.-F., Lefort V., Anisimova M., Hordijk W., Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3. 0. Syst. Biol. 59:307-321
    • (2010) Syst. Biol , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.-F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 56
    • 84880862788 scopus 로고    scopus 로고
    • Evolutionary biochemistry: Revealing the historical and physical causes of protein properties
    • Harms M. J., Thornton J. W. 2013. Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat. Rev. Genet. 14:559-571
    • (2013) Nat. Rev. Genet , vol.14 , pp. 559-571
    • Harms, M.J.1    Thornton, J.W.2
  • 57
    • 60549111699 scopus 로고    scopus 로고
    • Bayesian inference of population size history from multiple loci
    • Heled J., Drummond A. J. 2008. Bayesian inference of population size history from multiple loci. BMC Evol. Biol. 8:289
    • (2008) BMC Evol. Biol , vol.8 , pp. 289
    • Heled, J.1    Drummond, A.J.2
  • 58
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J., Drummond A. J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570
    • (2010) Mol. Biol. Evol , vol.27 , pp. 570
    • Heled, J.1    Drummond, A.J.2
  • 59
    • 77952294620 scopus 로고    scopus 로고
    • Isolation with migration moDels for more than two populations
    • Hey J. 2010. Isolation with migration moDels for more than two populations. Mol. Biol. Evol. 27:905-920
    • (2010) Mol. Biol. Evol , vol.27 , pp. 905-920
    • Hey, J.1
  • 60
    • 33847253975 scopus 로고    scopus 로고
    • Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics
    • Hey J., Nielsen R. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Nat. Acad. Sci. USA. 104:2785-2790
    • (2007) Proc. Nat. Acad. Sci. USA , vol.104 , pp. 2785-2790
    • Hey, J.1    Nielsen, R.2
  • 61
    • 33847253862 scopus 로고    scopus 로고
    • Genomic relationships and speciation times of human, Chimpanzee, and Gorilla inferred from a coalescent HidDen Markov moDel
    • Hobolth A., Christensen O. F., Mailund T., Schierup M. H. 2007. Genomic relationships and speciation times of human, Chimpanzee, and Gorilla inferred from a coalescent HidDen Markov moDel. PLoS Genet. 3:e7
    • (2007) PLoS Genet , vol.3 , pp. e7
    • Hobolth, A.1    Christensen, O.F.2    Mailund, T.3    Schierup, M.H.4
  • 62
    • 79952270485 scopus 로고    scopus 로고
    • Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and wiDespread selection
    • Hobolth A., Dutheil J. Y., Hawks J., Schierup M. H., Mailund T. 2011. Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and wiDespread selection. Genome Res. 21:349-356
    • (2011) Genome Res , vol.21 , pp. 349-356
    • Hobolth, A.1    Dutheil, J.Y.2    Hawks, J.3    Schierup, M.H.4    Mailund, T.5
  • 63
    • 84555188629 scopus 로고    scopus 로고
    • GuiDed tree topology proposals for Bayesian phylogenetic inference
    • Hna S., Drummond A. 2012. GuiDed tree topology proposals for Bayesian phylogenetic inference. Syst. Biol. 61:1-11
    • (2012) Syst. Biol , vol.61 , pp. 1-11
    • Hna, S.1    Drummond, A.2
  • 64
    • 28944447963 scopus 로고    scopus 로고
    • Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
    • HordijkW., Gascuel O. 2005. Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics 21:4338-4347
    • (2005) Bioinformatics , vol.21 , pp. 4338-4347
    • Hordijk, W.1    Gascuel, O.2
  • 65
    • 84876798186 scopus 로고    scopus 로고
    • The zebrafish reference genome sequence and its relationship to the human genome
    • Howe K. et al. 2013. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496:498-503
    • (2013) Nature , vol.496 , pp. 498-503
    • Howe, K.1
  • 68
    • 84876251356 scopus 로고    scopus 로고
    • Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting
    • Jones G., Sagitov S., Oxelman B. 2013. Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Syst. Biol. 62:467-478
    • (2013) Syst. Biol , vol.62 , pp. 467-478
    • Jones, G.1    Sagitov, S.2    Oxelman, B.3
  • 69
    • 63549118031 scopus 로고    scopus 로고
    • STEM: Species tree estimation using maximum likelihood for gene trees under coalescence
    • Kubatko L. S., Carstens B. C., Knowles L. L. 2009. STEM: species tree estimation using maximum likelihood for gene trees unDer coalescence. Bioinformatics 25:971-973
    • (2009) Bioinformatics , vol.25 , pp. 971-973
    • Kubatko, L.S.1    Carstens, B.C.2    Knowles, L.L.3
  • 70
    • 84866665369 scopus 로고    scopus 로고
    • An optimal reconciliation algorithmfor gene trees with polytomies
    • Lafond M., Swenson K. M., El-mabrouk N. 2012. An optimal reconciliation algorithmfor gene trees with polytomies. Algorithms Bioinformatics, p. 106-122
    • (2012) Algorithms Bioinformatics , pp. 106-122
    • Lafond, M.1    Swenson, K.M.2    El-Mabrouk, N.3
  • 73
    • 79960914105 scopus 로고    scopus 로고
    • Inference of human population history from individual whole-genome sequences
    • Li H., Durbin R. 2011. Inference of human population history from individual whole-genome sequences. Nature 475:493-496
    • (2011) Nature , vol.475 , pp. 493-496
    • Li, H.1    Durbin, R.2
  • 74
    • 34548575126 scopus 로고    scopus 로고
    • Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions
    • Liu L., Pearl D. K. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504-514
    • (2007) Syst. Biol , vol.56 , pp. 504-514
    • Liu, L.1    Pearl, D.K.2
  • 75
    • 47749093183 scopus 로고    scopus 로고
    • Estimating species trees using multiple-Allele DNA sequence data
    • Liu L., Pearl D. K., Brumfield R. T., Edwards S. V. 2008. Estimating species trees using multiple-Allele DNA sequence data. Evolution 62:2080-2091
    • (2008) Evolution , vol.62 , pp. 2080-2091
    • Liu, L.1    Pearl, D.K.2    Brumfield, R.T.3    Edwards, S.V.4
  • 76
    • 67649240664 scopus 로고    scopus 로고
    • Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
    • New York, NY
    • Liu K., Raghavan S., Nelesen S., LinDer C. R., Warnow T. 2009. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science (New York, NY), 324:1561-1564
    • (2009) Science , vol.324 , pp. 1561-1564
    • Liu, K.1    Raghavan, S.2    Nelesen, S.3    Linder, C.R.4    Warnow, T.5
  • 77
    • 80051975928 scopus 로고    scopus 로고
    • Estimating species trees from unrooted gene trees
    • Liu L., Yu L. 2011. Estimating species trees from unrooted gene trees. Syst. Biol. 60:661-667
    • (2011) Syst. Biol , vol.60 , pp. 661-667
    • Liu, L.1    Yu, L.2
  • 78
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent moDel
    • Liu L., Yu L., Edwards S. V. 2010. A maximum pseudo-likelihood approach for estimating species trees unDer the coalescent moDel. BMC Evol. Biol. 10:302
    • (2010) BMC Evol. Biol , vol.10 , pp. 302
    • Liu, L.1    Yu, L.2    Edwards, S.V.3
  • 79
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536
    • (1997) Syst. Biol , vol.46 , pp. 523-536
    • Maddison, W.P.1
  • 80
  • 81
    • 79953744766 scopus 로고    scopus 로고
    • Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidDen Markov moDel
    • Mailund T., Dutheil J. Y., Hobolth A., Lunter G., Schierup M. H. 2011. Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidDen Markov moDel. PLoS Genetics 7:e1001319
    • (2011) PLoS Genetics , vol.7 , pp. e1001319
    • Mailund, T.1    Dutheil, J.Y.2    Hobolth, A.3    Lunter, G.4    Schierup, M.H.5
  • 82
    • 77952679366 scopus 로고    scopus 로고
    • Ohnologs in the human genome are dosage balanced and frequently associated with disease
    • Makino T., McLysaght A. 2010. Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc. Nat. Acad. Sci. USA. 107:9270-9274
    • (2010) Proc. Nat. Acad. Sci. USA , vol.107 , pp. 9270-9274
    • Makino, T.1    McLysaght, A.2
  • 83
    • 50349088009 scopus 로고    scopus 로고
    • Phylogenetic Detection of recombination with a Bayesian prior on the distance between trees
    • Martins L. O., Leal E., Kishino H. 2008. Phylogenetic Detection of recombination with a Bayesian prior on the distance between trees. PLoS One 3:e2651
    • (2008) PLoS One , vol.3 , pp. e2651
    • Martins, L.O.1    Leal, E.2    Kishino, H.3
  • 84
    • 84873860010 scopus 로고    scopus 로고
    • A phylogeny of birds based on over 1, 500 loci collected by target enrichment and high-throughput sequencing
    • McCormack J. E., Harvey M. G., Faircloth B. C., Crawford N. G., Glenn T. C., Brumfield R. T. 2013. A phylogeny of birds based on over 1, 500 loci collected by target enrichment and high-throughput sequencing. PloS One, 8:e54848
    • (2013) PloS One , vol.8 , pp. e54848
    • McCormack, J.E.1    Harvey, M.G.2    Faircloth, B.C.3    Crawford, N.G.4    Glenn, T.C.5    Brumfield, R.T.6
  • 85
  • 86
    • 58249136809 scopus 로고    scopus 로고
    • Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A moDel
    • Meng C., Kubatko L. S. 2009. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A moDel. Theor. Popul. Biol. 75:35-45
    • (2009) Theor. Popul. Biol , vol.75 , pp. 35-45
    • Meng, C.1    Kubatko, L.S.2
  • 87
    • 79951749932 scopus 로고    scopus 로고
    • Bayesian sampling of genomic rearrangement scenarios via double cut and join
    • Mikl I., Tannier E. 2010. Bayesian sampling of genomic rearrangement scenarios via double cut and join. Bioinformatics. 26:3012-3019
    • (2010) Bioinformatics , vol.26 , pp. 3012-3019
    • Mikl, I.1    Tannier, E.2
  • 88
    • 45849122039 scopus 로고    scopus 로고
    • Smooth skyriDe through a rough skyline: Bayesian coalescent-based inference of population dynamics
    • Minin V. N., Bloomquist E. W., Suchard M. A. 2008. Smooth skyriDe through a rough skyline: Bayesian coalescent-based inference of population dynamics. Mol. Biol. Evol. 25:1459-1471
    • (2008) Mol. Biol. Evol , vol.25 , pp. 1459-1471
    • Minin, V.N.1    Bloomquist, E.W.2    Suchard, M.A.3
  • 89
    • 77957907040 scopus 로고    scopus 로고
    • Inferring the dynamics of diversification: A coalescent approach
    • Morlon H., Potts M. D., Plotkin J. B. 2009. Inferring the dynamics of diversification: a coalescent approach. PLoS Biol. 8(9
    • (2009) PLoS Biol , vol.8 , pp. 9
    • Morlon, H.1    Potts, M.D.2    Plotkin, J.B.3
  • 90
    • 77951972053 scopus 로고    scopus 로고
    • Genomicus: A database and a browser to study gene synteny in moDern and ancestral genomes
    • Muffato M., Louis A., Poisnel C.-E., Crollius H. R. 2010. Genomicus: a database and a browser to study gene synteny in moDern and ancestral genomes. Bioinformatics 26:1119
    • (2010) Bioinformatics , vol.26 , pp. 1119
    • Muffato, M.1    Louis, A.2    Poisnel, C.-E.3    Crollius, H.R.4
  • 92
    • 80053442046 scopus 로고    scopus 로고
    • Reconstructing the architecture of the ancestral amniote genome
    • Ouangraoua A., Tannier E., Chauve C. 2011. Reconstructing the architecture of the ancestral amniote genome. Bioinformatics. 27:2664-2671
    • (2011) Bioinformatics , vol.27 , pp. 2664-2671
    • Ouangraoua, A.1    Tannier, E.2    Chauve, C.3
  • 93
    • 0036365666 scopus 로고    scopus 로고
    • Vertebrate phylogenomics: Reconciled trees and gene duplications
    • Page R. D. M., Cotton J. A. 2002. Vertebrate phylogenomics: reconciled trees and gene duplications. Pac. Symp. Biocomput. p. 536-547
    • (2002) Pac. Symp. Biocomput , pp. 536-547
    • Page, R.D.M.1    Cotton, J.A.2
  • 94
    • 84928739261 scopus 로고
    • Librairie De Firmin Didot Fres). Rue Jacob, Paris
    • Pascal B. 1669. Oeuvres: les penses. (ed. 1830 Librairie De Firmin Didot Fres). Rue Jacob, Paris
    • (1669) Oeuvres: Les Penses , vol.1830
    • Pascal, B.1
  • 97
    • 33750437728 scopus 로고    scopus 로고
    • WiDespread discordance of gene trees with species tree in drosophila: EviDence for incomplete lineage sorting
    • Pollard D. A., Iyer V. N., Moses A. M., Eisen M. B. 2006. WiDespread discordance of gene trees with species tree in drosophila: eviDence for incomplete lineage sorting. PLoS Genet. 2:e173
    • (2006) PLoS Genet , vol.2 , pp. e173
    • Pollard, D.A.1    Iyer, V.N.2    Moses, A.M.3    Eisen, M.B.4
  • 98
    • 84890088964 scopus 로고    scopus 로고
    • Fpsac: Fast phylogenetic scaffolding of ancient contigs
    • Rajaraman A., Tannier E., Chauve C. 2013. Fpsac: fast phylogenetic scaffolding of ancient contigs. Bioinformatics. 29:2987-2994
    • (2013) Bioinformatics , vol.29 , pp. 2987-2994
    • Rajaraman, A.1    Tannier, E.2    Chauve, C.3
  • 99
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala B., Yang Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43:304-311
    • (1996) J. Mol. Evol , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 100
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes usingDNA sequences from multiple loci
    • Rannala B., Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes usingDNA sequences from multiple loci. Genetics 164:1645-1656
    • (2003) Genetics , vol.164 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 101
    • 84877090539 scopus 로고    scopus 로고
    • Improved reversible jump algorithms for Bayesian species Delimitation
    • Rannala B., Yang Z. 2013. Improved reversible jump algorithms for Bayesian species Delimitation. Genetics 194:245-253
    • (2013) Genetics , vol.194 , pp. 245-253
    • Rannala, B.1    Yang, Z.2
  • 102
    • 38849160068 scopus 로고    scopus 로고
    • Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes
    • Rasmussen M. D., Kellis M. 2007. Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes. Genome Res. 17:1932-1942
    • (2007) Genome Res , vol.17 , pp. 1932-1942
    • Rasmussen, M.D.1    Kellis, M.2
  • 103
    • 78650481676 scopus 로고    scopus 로고
    • A Bayesian approach for fast and accurate gene tree reconstruction
    • Rasmussen M. D., Kellis M. 2010. A Bayesian approach for fast and accurate gene tree reconstruction. Mol. Biol. Evol. 28:273-290
    • (2010) Mol. Biol. Evol , vol.28 , pp. 273-290
    • Rasmussen, M.D.1    Kellis, M.2
  • 104
    • 84859546516 scopus 로고    scopus 로고
    • Unified moDeling of gene duplication, loss, and coalescence using a locus tree
    • Rasmussen M. D., Kellis M. 2012. Unified moDeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 22:755-765
    • (2012) Genome Res , vol.22 , pp. 755-765
    • Rasmussen, M.D.1    Kellis, M.2
  • 105
    • 22844450838 scopus 로고    scopus 로고
    • Joint Bayesian estimation of alignment and phylogeny
    • ReDelings B., Suchard M. 2005. Joint Bayesian estimation of alignment and phylogeny. Syst. Biol. 54:401-418
    • (2005) Syst. Biol , vol.54 , pp. 401-418
    • Redelings, B.1    Suchard, M.2
  • 106
    • 84555186848 scopus 로고    scopus 로고
    • Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes
    • Reid N., Demboski J. R., Sullivan J. 2012. Phylogeny estimation of the radiation of western North American chipmunks (Tamias) in the face of introgression using reproductive protein genes. Syst. Biol. 61:44-62
    • (2012) Syst. Biol , vol.61 , pp. 44-62
    • Reid, N.1    Demboski, J.R.2    Sullivan, J.3
  • 107
    • 84871818181 scopus 로고    scopus 로고
    • Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands
    • Rocha S., Posada D., Harris D. J. 2013. Phylogeography and diversification history of the day-gecko genus Phelsuma in the Seychelles islands. BMC Evol. Biol. 13:3
    • (2013) BMC Evol. Biol , vol.13 , pp. 3
    • Rocha, S.1    Posada, D.2    Harris, D.J.3
  • 109
    • 0036245438 scopus 로고    scopus 로고
    • Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    • Rosenberg N. A., Nordborg M. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3:380-390
    • (2002) Nat. Rev. Genet , vol.3 , pp. 380-390
    • Rosenberg, N.A.1    Nordborg, M.2
  • 110
    • 70349205853 scopus 로고    scopus 로고
    • Bigfoot: Bayesian alignment and phylogenetic footprinting with mcmc
    • Satija R., Nov A., Mikl I., Lyngsa R., Hein J. 2009. Bigfoot: Bayesian alignment and phylogenetic footprinting with mcmc. BMC. Evol. Biol. 9:217
    • (2009) BMC. Evol. Biol , vol.9 , pp. 217
    • Satija, R.1    Nov, A.2    Mikl, I.3    Lyngsa, R.4    Hein, J.5
  • 111
    • 84863230553 scopus 로고    scopus 로고
    • Insights into hominid evolution from the gorilla genome sequence
    • Scally A. et al. 2012. Insights into hominid evolution from the gorilla genome sequence. Nature, 483:169-175
    • (2012) Nature , vol.483 , pp. 169-175
    • Scally, A.1
  • 112
    • 84883591070 scopus 로고    scopus 로고
    • Straw: Species tree analysis web server
    • Web Server issue
    • Shaw T. I., Ruan Z., Glenn T. C., Liu L. 2013. Straw: species tree analysis web server. Nucleic Acids Res. 41(Web Server issue):W238-W241
    • (2013) Nucleic Acids Res , vol.41 , pp. W238-W241
    • Shaw, T.I.1    Ruan, Z.2    Glenn, T.C.3    Liu, L.4
  • 115
    • 0031296691 scopus 로고    scopus 로고
    • Inferring species trees from gene trees: A phylogenetic analysis of the Elapidae (serpentes) based on the amino acid sequences of venom proteins
    • Slowinski J. B., Knight A., Rooney A. P. 1997. Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (serpentes) based on the amino acid sequences of venom proteins. Mol. Phylogenet. Evol. 8:349-362
    • (1997) Mol. Phylogenet. Evol , vol.8 , pp. 349-362
    • Slowinski, J.B.1    Knight, A.2    Rooney, A.P.3
  • 116
    • 84866289853 scopus 로고    scopus 로고
    • Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent moDel
    • Song S., Liu L., Edwards S., Wu S. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent moDel. Proc. Nat. Acad. Sci. 109:14942-14947
    • (2012) Proc. Nat. Acad. Sci , vol.109 , pp. 14942-14947
    • Song, S.1    Liu, L.2    Edwards, S.3    Wu, S.4
  • 117
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: A fast program formaximumlikelihood-based inference of large phylogenetic trees
    • Stamatakis A., Ludwig T., Meier H. 2005. RAxML-III: a fast program formaximumlikelihood-based inference of large phylogenetic trees. Bioinformatics. 21:456-463
    • (2005) Bioinformatics , vol.21 , pp. 456-463
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 118
    • 20444410815 scopus 로고    scopus 로고
    • Stochastic moDels for horizontal gene transfer: Taking a random walk through tree space
    • Suchard M. A. 2005. Stochastic moDels for horizontal gene transfer: taking a random walk through tree space. Genetics, 170:419-431
    • (2005) Genetics , vol.170 , pp. 419-431
    • Suchard, M.A.1
  • 119
    • 0036803331 scopus 로고    scopus 로고
    • Oh brother, where art thou A Bayes factor test for recombination with uncertain heritage
    • Suchard M. A., Weiss R. E., Dorman K. S., Sinsheimer J. S. 2002. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst. Biol. 51:715-728
    • (2002) Syst. Biol , vol.51 , pp. 715-728
    • Suchard, M.A.1    Weiss, R.E.2    Dorman, K.S.3    Sinsheimer, J.S.4
  • 120
    • 84860135294 scopus 로고    scopus 로고
    • MoDeling gene family evolution and reconciling phylogenetic discord
    • Szlosi G. J., Daubin V. 2012. MoDeling gene family evolution and reconciling phylogenetic discord. Methods Mol. Biol. 856:29-51
    • (2012) Methods Mol. Biol , vol.856 , pp. 29-51
    • Szlosi, G.J.1    Daubin, V.2
  • 121
    • 84867904826 scopus 로고    scopus 로고
    • Phylogenetic moDeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
    • Szlosi G. J., Boussau B., Abby S. S., Tannier E., Daubin V. 2012. Phylogenetic moDeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc. Nat. Acad. Sci. USA. 109:17513-17518
    • (2012) Proc. Nat. Acad. Sci. USA , vol.109 , pp. 17513-17518
    • Szlosi, G.J.1    Boussau, B.2    Abby, S.S.3    Tannier, E.4    Daubin, V.5
  • 124
    • 46249132832 scopus 로고    scopus 로고
    • Efficient inference of bacterial strain trees from genome-scale multilocus data
    • Than C., Sugino R., Innan H., Nakhleh L. 2008. Efficient inference of bacterial strain trees from genome-scale multilocus data. Bioinformatics 24:i123-i131
    • (2008) Bioinformatics , vol.24 , pp. i123-i131
    • Than, C.1    Sugino, R.2    Innan, H.3    Nakhleh, L.4
  • 125
    • 70349658769 scopus 로고    scopus 로고
    • Species tree inference by minimizing Deep coalescences
    • Than C., Nakhleh L. 2009. Species tree inference by minimizing Deep coalescences. PLoS Comput. Biol. 5:e1000501
    • (2009) PLoS Comput. Biol , vol.5 , pp. e1000501
    • Than, C.1    Nakhleh, L.2
  • 126
    • 34250380386 scopus 로고    scopus 로고
    • Confounding factors in HGT Detection: Statistical error, coalescent effects, and multiple solutions
    • Than C., Ruths D., Innan H., Nakhleh L. 2007. Confounding factors in HGT Detection: statistical error, coalescent effects, and multiple solutions. J. Comput. Biol. 14:517-535
    • (2007) J. Comput. Biol , vol.14 , pp. 517-535
    • Than, C.1    Ruths, D.2    Innan, H.3    Nakhleh, L.4
  • 127
    • 77953187312 scopus 로고    scopus 로고
    • Giga: A simple, efficient algorithm for gene tree inference in the genomic age
    • Thomas P. D. 2010. Giga: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics 11:312
    • (2010) BMC Bioinformatics , vol.11 , pp. 312
    • Thomas, P.D.1
  • 131
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara GeneTrees: Complete, duplication-Aware phylogenetic trees in vertebrates
    • Vilella A. J., Severin J., Ureta-Vidal A., Heng L., Durbin R., Birney E. 2008. EnsemblCompara GeneTrees: complete, duplication-Aware phylogenetic trees in vertebrates. Genome Res. 19:327-335
    • (2008) Genome Res , vol.19 , pp. 327-335
    • Vilella, A.J.1    Severin, J.2    Ureta-Vidal, A.3    Heng, L.4    Durbin, R.5    Birney, E.6
  • 133
    • 46249126320 scopus 로고    scopus 로고
    • DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
    • Wehe A., Bansal M. S., Burleigh J. G., Eulenstein O. 2008. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24:1540-1541
    • (2008) Bioinformatics , vol.24 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.S.2    Burleigh, J.G.3    Eulenstein, O.4
  • 134
    • 84857687426 scopus 로고    scopus 로고
    • Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood
    • Wu Y. 2011. Coalescent-based species tree inference from gene tree topologies unDer incomplete lineage sorting by maximum likelihood. Evol. 66:763-775
    • (2011) Evol , vol.66 , pp. 763-775
    • Wu, Y.1
  • 135
    • 84862907907 scopus 로고    scopus 로고
    • Evolution at the subgene level: Domain rearrangements in the drosophila phylogeny
    • Wu Y.-C., Rasmussen M. D., Kellis M. 2012. Evolution at the subgene level: domain rearrangements in the drosophila phylogeny. Mol. Biol. Evol. 29:689-705
    • (2012) Mol. Biol. Evol , vol.29 , pp. 689-705
    • Wu, Y.-C.1    Rasmussen, M.D.2    Kellis, M.3
  • 136
    • 84871822882 scopus 로고    scopus 로고
    • Treefix: Statistically informed gene tree error correction using species trees
    • Wu Y.-C., Rasmussen M. D., Bansal M. S., Kellis M. 2013. Treefix: statistically informed gene tree error correction using species trees. Syst. Biol. 62:110-120
    • (2013) Syst. Biol , vol.62 , pp. 110-120
    • Wu, Y.-C.1    Rasmussen, M.D.2    Bansal, M.S.3    Kellis, M.4
  • 137
    • 77952703002 scopus 로고    scopus 로고
    • Bayesian species Delimitation using multilocus sequence data
    • Yang Z., Rannala B. 2010. Bayesian species Delimitation using multilocus sequence data. Proc. Nat. Acad. Sci. USA. 107:9264-9269
    • (2010) Proc. Nat. Acad. Sci. USA , vol.107 , pp. 9264-9269
    • Yang, Z.1    Rannala, B.2
  • 138
    • 0037000637 scopus 로고    scopus 로고
    • Bayesian estimation of the number of inversions in the history of two chromosomes
    • York T. L., Durrett R., Nielsen R. 2002. Bayesian estimation of the number of inversions in the history of two chromosomes. J. Comput. Biol. 9:805-818
    • (2002) J. Comput. Biol , vol.9 , pp. 805-818
    • York, T.L.1    Durrett, R.2    Nielsen, R.3
  • 139
    • 84860577768 scopus 로고    scopus 로고
    • The probability of a gene tree topology within a phylogenetic network with applications to hybridization Detection
    • Yu Y., Degnan J. H., Nakhleh L. 2012. The probability of a gene tree topology within a phylogenetic network with applications to hybridization Detection. PLoS Genet. 8:e1002660
    • (2012) PLoS Genet , vol.8 , pp. e1002660
    • Yu, Y.1    Degnan, J.H.2    Nakhleh, L.3
  • 140
    • 84901287981 scopus 로고    scopus 로고
    • Fast algorithms and heuristics for phylogenomics under ils and hybridization
    • Yu Y., Ristic N., Nakhleh L. 2013. Fast algorithms and heuristics for phylogenomics unDer ils and hybridization. BMC Bioinformatics, 14:S6
    • (2013) BMC Bioinformatics , vol.14 , pp. S6
    • Yu, Y.1    Ristic, N.2    Nakhleh, L.3
  • 141
    • 1642339676 scopus 로고    scopus 로고
    • Cladogenesis, coalescence and the evolution of the three domains of life
    • Zhaxybayeva O., Gogarten J. P. 2004. Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet. 20:182-187
    • (2004) Trends Genet , vol.20 , pp. 182-187
    • Zhaxybayeva, O.1    Gogarten, J.P.2
  • 142
    • 0034791426 scopus 로고    scopus 로고
    • A simple algorithm to infer gene duplication and speciation events on a gene tree
    • Zmasek C. M., Eddy S. R. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17:821-828
    • (2001) Bioinformatics , vol.17 , pp. 821-828
    • Zmasek, C.M.1    Eddy, S.R.2


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