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Volumn 33, Issue 6, 2016, Pages 1590-1605

Clustering Genes of Common Evolutionary History

Author keywords

Clustering; Incomplete lineage sorting; Incongruence; Nonorthology; Phylogeny; Process agnostic

Indexed keywords

AGNOSTIC; ERROR; GENUS; HUMAN; PHYLOGENY; SPECIES; STATISTICAL MODEL; YEAST; BIOLOGICAL MODEL; CLUSTER ANALYSIS; COMPUTER SIMULATION; DNA SEQUENCE; EVOLUTION; GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PROCEDURES; SOFTWARE;

EID: 84973376091     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msw038     Document Type: Article
Times cited : (46)

References (88)
  • 1
    • 77954843377 scopus 로고    scopus 로고
    • Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
    • Abby SS, Tannier E, Gouy M, Daubin V. 2010. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics 11:324
    • (2010) BMC Bioinformatics , vol.11 , pp. 324
    • Abby, S.S.1    Tannier, E.2    Gouy, M.3    Daubin, V.4
  • 2
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Control. 19:716-723
    • (1974) IEEE Trans Automat Control , vol.19 , pp. 716-723
    • Akaike, H.1
  • 4
    • 80052014395 scopus 로고    scopus 로고
    • Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes
    • AnisimovaM, GilM,Dufayard JF, Dessimoz C, GascuelO. 2011. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol. 60:685-699
    • (2011) Syst Biol , vol.60 , pp. 685-699
    • Anisimova, M.1    Gil, M.2    Dufayard, J.F.3    Dessimoz, C.4    Gascuel, O.5
  • 5
    • 0000708831 scopus 로고
    • Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems
    • Antoniak CE. 1974. Mixtures of Dirichlet processes with applications to Bayesian nonparametric problems. Ann Stat. 2:1152-1174
    • (1974) Ann Stat , vol.2 , pp. 1152-1174
    • Antoniak, C.E.1
  • 6
    • 75149135738 scopus 로고    scopus 로고
    • Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
    • Bansal MS, Burleigh JG, Eulenstein O. 2010. Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinformatics 11(Suppl 1):S42
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 , pp. S42
    • Bansal, M.S.1    Burleigh, J.G.2    Eulenstein, O.3
  • 9
    • 13844266486 scopus 로고    scopus 로고
    • On the computational complexity of the rooted subtree prune and regraft distance
    • BordewichM, Semple C. 2005. On the computational complexity of the rooted subtree prune and regraft distance. Ann Comb. 8:409-423
    • (2005) Ann Comb , vol.8 , pp. 409-423
    • Bordewich, M.1    Semple, C.2
  • 12
    • 0033692378 scopus 로고    scopus 로고
    • NOTUNG: A program for dating gene duplications and optimizing gene family trees
    • Chen K, Durand D, Farach-Colton M. 2000. NOTUNG: a program for dating gene duplications and optimizing gene family trees. J Comput Biol. 7:429-447
    • (2000) J Comput Biol , vol.7 , pp. 429-447
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 13
    • 84894564007 scopus 로고    scopus 로고
    • Computing the joint distribution of tree shape and tree distance for gene tree inference and recombination detection
    • Chung Y, Perna NT, Ané C. 2013. Computing the joint distribution of tree shape and tree distance for gene tree inference and recombination detection. IEEE/ACM Trans Comput Biol Bioinform. 10:1263-1274
    • (2013) IEEE/ACM Trans Comput Biol Bioinform , vol.10 , pp. 1263-1274
    • Chung, Y.1    Perna, N.T.2    Ané, C.3
  • 14
    • 0030816742 scopus 로고    scopus 로고
    • Can three incongruence tests predict when data should be combined?
    • Cunningham CW. 1997. Can three incongruence tests predict when data should be combined? Mol Biol Evol. 14:733-740
    • (1997) Mol Biol Evol , vol.14 , pp. 733-740
    • Cunningham, C.W.1
  • 17
    • 33845627286 scopus 로고    scopus 로고
    • The supermatrix approach to systematics
    • de Queiroz A, Gatesy J. 2007. The supermatrix approach to systematics. Trends Ecol Evol. 22:34-41
    • (2007) Trends Ecol Evol , vol.22 , pp. 34-41
    • De Queiroz, A.1    Gatesy, J.2
  • 18
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375
    • (2005) Nat Rev Genet , vol.6 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 19
    • 0036368057 scopus 로고    scopus 로고
    • Speciation in the globeflower fly Chiastocheta spp (Diptera: Anthomyiidae) in relation to host plant species, biogeography, and morphology
    • Després L, Pettex E, Plaisance V, Pompanon F. 2002. Speciation in the globeflower fly Chiastocheta spp. (Diptera: Anthomyiidae) in relation to host plant species, biogeography, and morphology. Mol Phylogenet Evol. 22:258-268
    • (2002) Mol Phylogenet Evol , vol.22 , pp. 258-268
    • Després, L.1    Pettex, E.2    Plaisance, V.3    Pompanon, F.4
  • 20
    • 47249164436 scopus 로고    scopus 로고
    • DLIGHT-lateral gene transfer detection using pairwise evolutionary distances in a statistical framework
    • Vingron M, Wong L, editors. Berlin Heidelberg (Germany): Springer
    • Dessimoz C, Margadant D, Gonnet GH. 2008. DLIGHT-lateral gene transfer detection using pairwise evolutionary distances in a statistical framework. In: Vingron M, Wong L, editors. Research in computational molecular biology, Lecture Notes in Computer science. Berlin Heidelberg (Germany): Springer. p. 315-330
    • (2008) Research in Computational Molecular Biology, Lecture Notes in Computer Science , pp. 315-330
    • Dessimoz, C.1    Margadant, D.2    Gonnet, G.H.3
  • 21
    • 78649930876 scopus 로고    scopus 로고
    • An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers
    • Tannier E, editor. Berlin Heidelberg (Germany): Springer
    • Doyon JP, Scornavacca C, Gorbunov KY, Szöllosi GJ, Ranwez V, Berry V. 2010. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. In: Tannier E, editor. Comparative genomics. Lecture Notes in Computer Science. Berlin Heidelberg (Germany): Springer. p. 93-108
    • (2010) Comparative Genomics. Lecture Notes in Computer Science , pp. 93-108
    • Doyon, J.P.1    Scornavacca, C.2    Gorbunov, K.Y.3    Szöllosi, G.J.4    Ranwez, V.5    Berry, V.6
  • 22
    • 77953754620 scopus 로고    scopus 로고
    • Yeast evolutionary genomics
    • Dujon B. 2010. Yeast evolutionary genomics. Nat Rev Genet. 11:512-524
    • (2010) Nat Rev Genet , vol.11 , pp. 512-524
    • Dujon, B.1
  • 23
    • 84903726447 scopus 로고    scopus 로고
    • PyRAD: Assembly of de novo RADseq loci for phylogenetic analyses
    • Eaton DAR. 2014. PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics 30:1844-1849
    • (2014) Bioinformatics , vol.30 , pp. 1844-1849
    • Eaton, D.A.R.1
  • 24
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 25
    • 84858076219 scopus 로고    scopus 로고
    • Ecological and historical drivers of diversification in the fly genus Chiastocheta Pokorny
    • Espíndola A, Buerki S, Alvarez N. 2012. Ecological and historical drivers of diversification in the fly genus Chiastocheta Pokorny. Mol Phylogenet Evol. 63:466-474
    • (2012) Mol Phylogenet Evol , vol.63 , pp. 466-474
    • Espíndola, A.1    Buerki, S.2    Alvarez, N.3
  • 26
    • 84959752542 scopus 로고
    • Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units
    • Estabrook GF, McMorris FR, Meacham CA. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst Biol. 34:193-200
    • (1985) Syst Biol , vol.34 , pp. 193-200
    • Estabrook, G.F.1    McMorris, F.R.2    Meacham, C.A.3
  • 27
    • 85170282443 scopus 로고    scopus 로고
    • A density-based algorithm for discovering clusters in large spatial databases with noise
    • Simoudis E, Han J, Fayyad U, editors. AAAI Press
    • Ester M, Kriegel HP, Sander J, Xu X. 1996. A density-based algorithm for discovering clusters in large spatial databases with noise. In: Simoudis E, Han J, Fayyad U, editors. Second International Conference on Knowledge Discovery and Data Mining. AAAI Press. p. 226-231
    • (1996) Second International Conference on Knowledge Discovery and Data Mining , pp. 226-231
    • Ester, M.1    Kriegel, H.P.2    Sander, J.3    Xu, X.4
  • 29
    • 84969545748 scopus 로고
    • A Bayesian analysis of some nonparametric problems
    • Ferguson TS. 1973. A Bayesian analysis of some nonparametric problems. Ann Stat. 1:209-230
    • (1973) Ann Stat , vol.1 , pp. 209-230
    • Ferguson, T.S.1
  • 32
    • 33847172327 scopus 로고    scopus 로고
    • Clustering by passing messages between data points
    • Frey BJ, Dueck D. 2007. Clustering by passing messages between data points. Science 315:972-976
    • (2007) Science , vol.315 , pp. 972-976
    • Frey, B.J.1    Dueck, D.2
  • 33
    • 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
  • 34
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • Goldman N. 1993. Statistical tests of models of DNA substitution. J Mol Evol. 36:182-198
    • (1993) J Mol Evol , vol.36 , pp. 182-198
    • Goldman, N.1
  • 35
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman N, Thorne JL, Jones DT. 1998. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149:445-458
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 38
    • 77249086587 scopus 로고    scopus 로고
    • Bayesian inference of species trees from multilocus data
    • Heled J, Drummond AJ. 2010. Bayesian inference of species trees from multilocus data.Mol Biol Evol. 27:570-580
    • (2010) Mol Biol Evol , vol.27 , pp. 570-580
    • Heled, J.1    Drummond, A.J.2
  • 39
    • 79961133759 scopus 로고    scopus 로고
    • Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: Yeasts revisited
    • Hess J, Goldman N. 2011. Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited. PLoS One 6:e22783
    • (2011) PLoS One , vol.6 , pp. e22783
    • Hess, J.1    Goldman, N.2
  • 40
    • 12044255616 scopus 로고
    • Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis?
    • Huelsenbeck JP, Swofford DL, Cunningham CW, Bull JJ,Waddell PJ. 1994. Is character weighting a panacea for the problem of data heterogeneity in phylogenetic analysis? Syst Biol. 43:288-291
    • (1994) Syst Biol , vol.43 , pp. 288-291
    • Huelsenbeck, J.P.1    Swofford, D.L.2    Cunningham, C.W.3    Bull, J.J.4    Waddell, P.J.5
  • 42
    • 0016287617 scopus 로고
    • Statistical estimation of parameters in a phylogenetic tree using a dynamic model of the substitutional process
    • Kashyap RL, Subas S. 1974. Statistical estimation of parameters in a phylogenetic tree using a dynamic model of the substitutional process. J Theor Biol. 47:75-101
    • (1974) J Theor Biol , vol.47 , pp. 75-101
    • Kashyap, R.L.1    Subas, S.2
  • 45
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • Kuhner MK, Felsenstein J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol. 11:459-468
    • (1994) Mol Biol Evol , vol.11 , pp. 459-468
    • Kuhner, M.K.1    Felsenstein, J.2
  • 46
    • 84861380450 scopus 로고    scopus 로고
    • Partitionfinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses
    • Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.Mol Biol Evol. 29:1695-1701
    • (2012) Mol Biol Evol , vol.29 , pp. 1695-1701
    • Lanfear, R.1    Calcott, B.2    Ho, S.Y.W.3    Guindon, S.4
  • 47
    • 78149256307 scopus 로고    scopus 로고
    • BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
    • Larget BR, Kotha SK, Dewey CN, Ané C. 2010. BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics 26:2910-2911
    • (2010) Bioinformatics , vol.26 , pp. 2910-2911
    • Larget, B.R.1    Kotha, S.K.2    Dewey, C.N.3    Ané, C.4
  • 49
    • 80051792622 scopus 로고    scopus 로고
    • Let them fall where they may: Congruence analysis in massive phylogenetically messy data sets
    • Leigh JW, Schliep K, Lopez P, Bapteste E. 2011. Let them fall where they may: congruence analysis in massive phylogenetically messy data sets. Mol Biol Evol. 28:2773-2785
    • (2011) Mol Biol Evol , vol.28 , pp. 2773-2785
    • Leigh, J.W.1    Schliep, K.2    Lopez, P.3    Bapteste, E.4
  • 52
    • 84932109367 scopus 로고    scopus 로고
    • Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference
    • Mastretta-Yanes A, Arrigo N, Alvarez N, Jorgensen TH, Pinero D, Emerson BC. 2015. Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference. Mol Ecol Resour. 15:28-41
    • (2015) Mol Ecol Resour , vol.15 , pp. 28-41
    • Mastretta-Yanes, A.1    Arrigo, N.2    Alvarez, N.3    Jorgensen, T.H.4    Pinero, D.5    Emerson, B.C.6
  • 53
    • 33947156744 scopus 로고    scopus 로고
    • Comparing clusterings-an information based distance
    • MeiláM. 2007. Comparing clusterings-an information based distance. J Multivar Anal. 98:873-895
    • (2007) J Multivar Anal , vol.98 , pp. 873-895
    • Meilá, M.1
  • 54
    • 84917708481 scopus 로고    scopus 로고
    • Statistical binning enables an accurate coalescent-based estimation of the avian tree
    • Mirarab S, Bayzid MS, Boussau B, Warnow T. 2014. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 346:1250463
    • (2014) Science , vol.346 , pp. 1250463
    • Mirarab, S.1    Bayzid, M.S.2    Boussau, B.3    Warnow, T.4
  • 55
    • 84878460994 scopus 로고    scopus 로고
    • Fastcluster: Fast hierarchical, agglomerative clustering routines for R and Python
    • Müllner D. 2013. fastcluster: fast hierarchical, agglomerative clustering routines for R and Python. J Stat Softw. 53:1-18
    • (2013) J Stat Softw , vol.53 , pp. 1-18
    • Müllner, D.1
  • 56
    • 84888385201 scopus 로고    scopus 로고
    • PhyBin: Binning trees by topology
    • Newton RR, Newton ILG. 2013. PhyBin: binning trees by topology. PeerJ 1:e187
    • (2013) PeerJ , vol.1 , pp. e187
    • Newton, R.R.1    Newton, I.L.G.2
  • 57
    • 0001879933 scopus 로고
    • Molecular studies of evolution: A source of novel statistical problems
    • Gupta SS, Yackel J, editors. New York: Academic Press
    • Neyman J. 1971. Molecular studies of evolution: a source of novel statistical problems. In: Gupta SS, Yackel J, editors. Statistical decision theory and related topics. New York: Academic Press. p. 1-27
    • (1971) Statistical Decision Theory and Related Topics , pp. 1-27
    • Neyman, J.1
  • 58
    • 0041875229 scopus 로고    scopus 로고
    • On spectral clustering: Analysis and an algorithm
    • Dietterich T, Becker S, Ghahramani Z, editors. MIT Press
    • Ng AY, Jordan MI, Weiss Y. 2001. On spectral clustering: analysis and an algorithm. In: Dietterich T, Becker S, Ghahramani Z, editors. Advances in neural information processing system. Vol. 2. MIT Press. p. 849-856
    • (2001) Advances in Neural Information Processing System , vol.2 , pp. 849-856
    • Ng, A.Y.1    Jordan, M.I.2    Weiss, Y.3
  • 59
    • 47249109137 scopus 로고    scopus 로고
    • Trees of trees: An approach to comparing multiple alternative phylogenies
    • Nye TMW. 2008. Trees of trees: an approach to comparing multiple alternative phylogenies. Syst Biol. 57:785-794
    • (2008) Syst Biol , vol.57 , pp. 785-794
    • Nye, T.M.W.1
  • 60
    • 78449288503 scopus 로고    scopus 로고
    • A fast algorithm for computing geodesic distances in tree space
    • Owen M, Provan JS. 2011. A fast algorithm for computing geodesic distances in tree space. IEEE/ACM Trans Comput Biol Bioinform. 8:2-13
    • (2011) IEEE/ACM Trans Comput Biol Bioinform , vol.8 , pp. 2-13
    • Owen, M.1    Provan, J.S.2
  • 61
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Mol Biol Evol. 5:568-583
    • (1988) Mol Biol Evol , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 64
    • 0027012319 scopus 로고
    • The phylogeny of a mutualism: Evolution and coadaptation between Trollius and its seed-parasitic pollinators
    • Pellmyr O. 1992. The phylogeny of a mutualism: evolution and coadaptation between Trollius and its seed-parasitic pollinators. Biol J Linn Soc Lond. 47:337-365
    • (1992) Biol J Linn Soc Lond , vol.47 , pp. 337-365
    • Pellmyr, O.1
  • 65
    • 84861691274 scopus 로고    scopus 로고
    • Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species
    • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135
    • (2012) PLoS One , vol.7 , pp. e37135
    • Peterson, B.K.1    Weber, J.N.2    Kay, E.H.3    Fisher, H.S.4    Hoekstra, H.E.5
  • 67
    • 31344454068 scopus 로고    scopus 로고
    • Tree disagreement: Measuring and testing incongruence in phylogenies
    • Planet PJ. 2006. Tree disagreement: measuring and testing incongruence in phylogenies. J Biomed Inform. 39:86-102
    • (2006) J Biomed Inform , vol.39 , pp. 86-102
    • Planet, P.J.1
  • 68
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala B, Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656
    • (2003) Genetics , vol.164 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.2
  • 69
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson DF, Foulds LR. 1981. Comparison of phylogenetic trees. Math Biosci. 53:131-147
    • (1981) Math Biosci , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 70
    • 0023453329 scopus 로고
    • Silhouettes: A graphical aid to the interpretation and validation of cluster analysis
    • Rousseeuw PJ. 1987. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math. 20:53-65
    • (1987) J Comput Appl Math , vol.20 , pp. 53-65
    • Rousseeuw, P.J.1
  • 71
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 72
    • 84973357494 scopus 로고
    • Estimating the dimension of a model
    • Schwarz G. 1978. Estimating the dimension of a model. Ann Stat. 6:461-464
    • (1978) Ann Stat , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 73
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 74
    • 84946487244 scopus 로고    scopus 로고
    • Asymmetrical nature of the Trollius-Chiastocheta interaction: Insights into the evolution of nursery pollination systems
    • Suchan T, Beauverd M, Trim N, Alvarez N. 2015. Asymmetrical nature of the Trollius-Chiastocheta interaction: insights into the evolution of nursery pollination systems. Ecol Evol. 5:4766-4777
    • (2015) Ecol Evol , vol.5 , pp. 4766-4777
    • Suchan, T.1    Beauverd, M.2    Trim, N.3    Alvarez, N.4
  • 75
    • 77954202497 scopus 로고    scopus 로고
    • DendroPy: A Python library for phylogenetic computing
    • Sukumaran J, Holder MT. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26:1569-1571
    • (2010) Bioinformatics , vol.26 , pp. 1569-1571
    • Sukumaran, J.1    Holder, M.T.2
  • 76
    • 84860135294 scopus 로고    scopus 로고
    • Modeling gene family evolution and reconciling phylogenetic discord
    • Szöllosi GJ, 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
    • Szöllosi, G.J.1    Daubin, V.2
  • 77
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Miura RM, editor. Providence (RI): American Mathematic Society
    • Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura RM, editor. Lectures onmathematics in the life sciences. Vol. 17. Providence (RI): American Mathematic Society. p. 57-86
    • (1986) Lectures Onmathematics in the Life Sciences , vol.17 , pp. 57-86
    • Tavaré, S.1
  • 78
    • 84950351930 scopus 로고
    • Multidimensional scaling: I Theory and method
    • Torgerson WS. 1952. Multidimensional scaling: I. Theory and method. Psychometrika 17:401-419
    • (1952) Psychometrika , vol.17 , pp. 401-419
    • Torgerson, W.S.1
  • 79
    • 0033635534 scopus 로고    scopus 로고
    • Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests
    • Waddell PJ, Kishino H, Ota R. 2000. Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests. Mol Biol Evol. 17:1988-1992
    • (2000) Mol Biol Evol , vol.17 , pp. 1988-1992
    • Waddell, P.J.1    Kishino, H.2    Ota, R.3
  • 80
    • 38149146221 scopus 로고
    • Tree compatibility and inferring evolutionary history
    • Warnow TJ. 1994. Tree compatibility and inferring evolutionary history. J Algorithm Comput Technol. 16:388-407
    • (1994) J Algorithm Comput Technol , vol.16 , pp. 388-407
    • Warnow, T.J.1
  • 81
    • 84861373817 scopus 로고    scopus 로고
    • Concatenation and concordance in the reconstruction of mouse lemur phylogeny: An empirical demonstration of the effect of allele sampling in phylogenetics
    • Weisrock DW, Smith SD, Chan LM, Biebouw K, Kappeler PM, Yoder AD. 2012. Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics. Mol Biol Evol. 29:1615-1630
    • (2012) Mol Biol Evol , vol.29 , pp. 1615-1630
    • Weisrock, D.W.1    Smith, S.D.2    Chan, L.M.3    Biebouw, K.4    Kappeler, P.M.5    Yoder, A.D.6
  • 83
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol. 18:691-699
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 84
    • 84884945088 scopus 로고    scopus 로고
    • Fixed-parameter algorithms for maximum agreement forests
    • Whidden C, Beiko RG, Zeh N. 2013. Fixed-parameter algorithms for maximum agreement forests. SIAM J Comput. 42:1431-1466
    • (2013) SIAM J Comput , vol.42 , pp. 1431-1466
    • Whidden, C.1    Beiko, R.G.2    Zeh, N.3
  • 85
    • 0001972601 scopus 로고
    • The large-sample distribution of the likelihood ratio for testing composite hypotheses
    • Wilks SS. 1938. The large-sample distribution of the likelihood ratio for testing composite hypotheses. Ann Math Stat. 9:60-62
    • (1938) Ann Math Stat , vol.9 , pp. 60-62
    • Wilks, S.S.1
  • 86
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximatemethods
    • Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximatemethods. J Mol Evol. 39:306-314
    • (1994) J Mol Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 87
    • 0001778604 scopus 로고
    • A mathematical theory of evolution, based on the conclusions
    • Dr. JC Willis, FRS
    • Yule GU. 1925. A mathematical theory of evolution, based on the conclusions of Dr. JC Willis, FRS. Philos Trans R Soc Lond B 213:21-87
    • (1925) Philos Trans R Soc Lond B , vol.213 , pp. 21-87
    • Yule, G.U.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.