메뉴 건너뛰기




Volumn 55, Issue 5, 2006, Pages 740-755

SDM: A fast distance-based approach for (super)tree building in phylogenomics

Author keywords

Distance method; Evolutionary distances; MRP; Phylogenomics; Supermatrix; Supertree; Total evidence

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; CLASSIFICATION; COMPUTER SIMULATION; EVALUATION; GENOMICS; METHODOLOGY; PHYLOGENY;

EID: 34447341925     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150600969872     Document Type: Article
Times cited : (62)

References (76)
  • 1
    • 33745256005 scopus 로고    scopus 로고
    • Approximate likelihood ratio test for branches: A fast, accurate and powerful alternative
    • in press
    • Anisimova, M., and O. Gascuel. 2006. Approximate likelihood ratio test for branches: A fast, accurate and powerful alternative. Syst. Biol. in press.
    • (2006) Syst. Biol.
    • Anisimova, M.1    Gascuel, O.2
  • 3
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
    • Baum, B. R. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10.
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.R.1
  • 4
    • 0029794480 scopus 로고    scopus 로고
    • On the interpretation of bootstrap trees: Appropriate threshold of clade selection and induced gain
    • Berry, V., and O. Gascuel. 1996. Interpretation of bootstrap trees: Threes-hold of clade selection and induced gain. Mol. Biol. Evol. 13:999-1011. (Pubitemid 26284916)
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.7 , pp. 999-1011
    • Berry, V.1    Gascuel, O.2
  • 5
    • 33644828849 scopus 로고    scopus 로고
    • Calculating the evolutionary rates of different genes: A fast, accurate estimator with applications to maximum likelihood phylogenetic analysis
    • Bevan, R. B., B. F. Lang, and D. Bryant. 2005. Calculating the evolutionary rates of different genes: A fast, accurate estimator with applications to maximum likelihood phylogenetic analysis. Syst. Biol. 54:900-915.
    • (2005) Syst. Biol. , vol.54 , pp. 900-915
    • Bevan, R.B.1    Lang, B.F.2    Bryant, D.3
  • 7
    • 0032148631 scopus 로고    scopus 로고
    • Properties of Matrix Representation with Parsimony Analyses
    • Bininda-Emonds, O. R. P., and H. N. Bryant. 1998. Properties of matrix representation with parsimony analyses. Syst. Biol. 47:497-508. (Pubitemid 128451088)
    • (1998) Systematic Biology , vol.47 , Issue.3 , pp. 497-508
    • Bininda-Emonds, O.R.P.1    Bryant, H.N.2
  • 8
    • 0035527411 scopus 로고    scopus 로고
    • Assessment of the accuracy of matrix representation with parsimony supertree construction
    • Bininda-Emonds, O. R. P., and M. J. Sanderson. 2001. Assessment of the accuracy of matrix representation with parsimony supertree construction. Syst. Biol. 50:565-579.
    • (2001) Syst. Biol. , vol.50 , pp. 565-579
    • Bininda-Emonds, O.R.P.1    Sanderson, M.J.2
  • 10
    • 1642519173 scopus 로고    scopus 로고
    • A classification of consensus methods for phylogenetics
    • (M. Janowitz, F.-J. Lapointe, F. R. McMorris, B. Mirkin, F. S. Roberts, eds.). DIMACS-AMS edition, Providence
    • Bryant, D. 2001. A classification of consensus methods for phylogenetics. Pages 163-184 in Bioconsensus (M. Janowitz, F.-J. Lapointe, F. R. McMorris, B. Mirkin, F. S. Roberts, eds.). DIMACS-AMS edition, Providence.
    • (2001) Bioconsensus , pp. 163-184
    • Bryant, D.1
  • 11
    • 13844250623 scopus 로고    scopus 로고
    • Clann: Investigating phylogenetic information through supertree analyses
    • DOI 10.1093/bioinformatics/bti020
    • Creevey, C. J. and J. O. Mclnerney. 2005. Clann: Investigating phylogenetic information through supertree analyses. Bioinformatics 21:390-392. (Pubitemid 40246612)
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 390-392
    • Creevey, C.J.1    McInerney, J.O.2
  • 12
    • 0036061865 scopus 로고    scopus 로고
    • A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history
    • DOI 10.1101/gr.187002
    • Daubin, V., M. Gouy, and G. Perriere. 2002. A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res. 12:1080-1090. (Pubitemid 34785201)
    • (2002) Genome Research , vol.12 , Issue.7 , pp. 1080-1090
    • Daubin, V.1    Gouy, M.2    Perriere, G.3
  • 13
    • 0000355328 scopus 로고
    • Additive tree representations of incomplete dissimilarity data
    • De Soete, G. 1984. Additive tree representations of incomplete dissimilarity data. Quality Quantity 18:387-393.
    • (1984) Quality Quantity , vol.18 , pp. 387-393
    • De Soete, G.1
  • 14
    • 0036943052 scopus 로고    scopus 로고
    • Fast and accurate phylogeny reconstruction algorithms based on the Minimum-Evolution principle
    • DOI 10.1089/106652702761034136
    • Desper, R., and O. Gascuel. 2002. Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comp. Biol. 19:687-705. (Pubitemid 36042994)
    • (2002) Journal of Computational Biology , vol.9 , Issue.5 , pp. 687-705
    • Desper, R.1    Gascuel, O.2
  • 16
    • 8444222732 scopus 로고    scopus 로고
    • Prospects for building the tree of life from large sequence databases
    • DOI 10.1126/science.1102036
    • Driskell, A. C, C. Ané, J. G. Burleigh, M. M. McMahon, B. C. O'Meara, and M. J. Sanderson. 2004. Pospects for building the tree of life from large sequence databases. Science 306:1172-1174. (Pubitemid 39488993)
    • (2004) Science , vol.306 , Issue.5699 , pp. 1172-1174
    • Driskell, A.C.1    Ane, C.2    Burleig, J.G.3    McMahon, M.M.4    O'Meara, B.C.5    Sanderson, M.J.6
  • 17
    • 0038518196 scopus 로고    scopus 로고
    • Phylogenomics: Intersection of evolution and genomics
    • DOI 10.1126/science.1086292
    • Eisen, J. A., and C. M. Fraser. 2003. Phylogenomics: Intersection of evolution and genomics. Science 300:1706-1707. (Pubitemid 36712558)
    • (2003) Science , vol.300 , Issue.5626 , pp. 1706-1707
    • Eisen, J.A.1    Fraser, C.M.2
  • 18
    • 84959752542 scopus 로고
    • Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units
    • Estabrook, G. F., F. R. McMorris, and C. A. Meacham. 1985. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Syst. Zool. 34:193-200.
    • (1985) Syst. Zool. , vol.34 , pp. 193-200
    • Estabrook, G.F.1    McMorris, F.R.2    Meacham, C.A.3
  • 19
    • 2442598026 scopus 로고    scopus 로고
    • Performance of flip supertree construction with a heuristic algorithm
    • DOI 10.1080/10635150490423719
    • Eulenstein, O., D. Chen, J. G. Burleigh, D. Fernandez-Baca, and M. J. Sanderson. 2004. Performance of flip supertree construction with a heuristic algorithm. Syst. Biol. 53:299-308. (Pubitemid 38611184)
    • (2004) Systematic Biology , vol.53 , Issue.2 , pp. 299-308
    • Eulenstein, O.1    Chen, D.2    Burleih, J.G.3    Fernandez-Baca, D.4    Sanderson, M.J.5
  • 20
    • 0029192324 scopus 로고
    • A robust model for finding optimal evolutionary trees
    • Farach, M., S. Kannan, and T. Warnow. 1995. A robust model for finding optimal evolutionary trees. Algorithmica 13:155-179.
    • (1995) Algorithmica , vol.13 , pp. 155-179
    • Farach, M.1    Kannan, S.2    Warnow, T.3
  • 21
    • 0003437299 scopus 로고
    • version 3.6b. Distributed by the author. University of Washington, Seattle
    • Felsenstein, J. 1993. Phylip: Phylogeny inference package, version 3.6b. Distributed by the author. University of Washington, Seattle.
    • (1993) Phylip: Phylogeny Inference Package
    • Felsenstein, J.1
  • 22
    • 0031084471 scopus 로고    scopus 로고
    • An alternating least squares approach to inferring phylogenies from pairwise distances
    • Felsenstein, J. 1997. An alternating least-squares approach to inferring phylogenies. Syst. Biol. 46:101-111. (Pubitemid 127365610)
    • (1997) Systematic Biology , vol.46 , Issue.1 , pp. 101-111
    • Felsenstein, J.1
  • 23
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • Fitch, W. M., and E. Margoliash. 1967. Construction of phylogenetic trees. Science 155:279-284.
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 24
    • 0028035267 scopus 로고
    • A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances [1]
    • Gascuel, O. 1994. A note on Sattath and Tversky's, Saitou and Nei's and Studier and Keppler's algorithms for inferring phylogenies from evolutionary distances. Mol. Biol. Evol. 11:961-963. (Pubitemid 24349477)
    • (1994) Molecular Biology and Evolution , vol.11 , Issue.6 , pp. 961-963
    • Gascuel, O.1
  • 25
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel, O. 1997. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14:685-695. (Pubitemid 27287289)
    • (1997) Molecular Biology and Evolution , vol.14 , Issue.7 , pp. 685-695
    • Gascuel, O.1
  • 26
    • 0036698966 scopus 로고    scopus 로고
    • Resolution of a supertree/supermatrix paradox
    • DOI 10.1080/10635150290102311
    • Gatesy, J., C. Matthee, R. DeSalle, and C. Hayashi. 2002. Resolution of a supertree/supermatrix paradox. Syst. Biol. 51:652-664. (Pubitemid 35180694)
    • (2002) Systematic Biology , vol.51 , Issue.4 , pp. 652-664
    • Gatesy, J.1    Matthee, C.2    Desalle, R.3    Hayashi, C.4
  • 28
    • 0002094303 scopus 로고    scopus 로고
    • Approximations par arbre d'une distance partielle
    • Guénoche, A., and S. Grandcolas. 1999. Approximations par arbre d'une distance partielle. Math. Inf. Sci. Humaines, 146:51-64.
    • (1999) Math. Inf. Sci. Humaines , vol.146 , pp. 51-64
    • Guénoche, A.1    Grandcolas, S.2
  • 29
    • 0242578620 scopus 로고    scopus 로고
    • A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
    • DOI 10.1080/10635150390235520
    • Guindon, S., and O. Gascuel. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704. (Pubitemid 37365050)
    • (2003) Systematic Biology , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 30
    • 84960586331 scopus 로고    scopus 로고
    • When are fossils better than extant taxa in phylogenetic analysis?
    • Huelsenbeck, J. P. 2001. When are fossils better than extant taxa in phylogenetic analysis? Syst. Zool. 40:458-469.
    • (2001) Syst. Zool. , vol.40 , pp. 458-469
    • Huelsenbeck, J.P.1
  • 31
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P. and F. Ronquist. 2001. MrBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755. (Pubitemid 32851390)
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 32
    • 0032746022 scopus 로고    scopus 로고
    • Disk-covering, a fast-converging method for phylogenetic tree reconstruction
    • Huson, D. H., S. M. Nettles and T. J. Warnow. 1999. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comp. Biol. 6:369-386.
    • (1999) J. Comp. Biol. , vol.6 , pp. 369-386
    • Huson, D.H.1    Nettles, S.M.2    Warnow, T.J.3
  • 33
    • 0036554650 scopus 로고    scopus 로고
    • Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions
    • DOI 10.1080/10635150252899824
    • Kearney, M. 2002. Fragmentary taxa, missing data, and ambiguity: Mistaken assumptions and conclusions. Syst. Biol. 51:369-381. (Pubitemid 35180714)
    • (2002) Systematic Biology , vol.51 , Issue.2 , pp. 369-381
    • Kearney, M.1
  • 34
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • DOI 10.1007/BF01731581
    • Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120. (Pubitemid 11166431)
    • (1980) Journal of Molecular Evolution , vol.16 , Issue.2 , pp. 111-120
    • Kimura, M.1
  • 35
    • 0025181359 scopus 로고
    • Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
    • DOI 10.1007/BF02109483
    • Kishino, H., T. Miyata, and M. Hasegawa. 1990. Maximum likelihood inference of protein phylogeny ans the origin of chloroplasts. J. Mol. Evol. 31:151-160. (Pubitemid 20261943)
    • (1990) Journal of Molecular Evolution , vol.31 , Issue.2 , pp. 151-160
    • Kishino, H.1    Miyata, T.2    Hasegawa, M.3
  • 36
    • 0029999779 scopus 로고    scopus 로고
    • Estimating phylogenies from lacunose distance matrices: Additive is superior to ultrametric estimation
    • Landry, P.-A., F.-J. Lapointe, and J. A. W. Kirsch. 1996. Estimating phylogenies from lacunose distance matrices: Additive is superior to ultrametric estimation. Mol. Biol. Evol. 13:818-823. (Pubitemid 26240086)
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.6 , pp. 818-823
    • Landry, P.-A.1    Lapointe, F.-J.2    Kirsch, J.A.W.3
  • 37
    • 0031513152 scopus 로고    scopus 로고
    • The Average Consensus Procedure: Combination of Weighted Trees Containing Identical or Overlapping Sets of Taxa
    • Lapointe, F.-J., and G. Cucumel. 1997. The average consensus procedure: Combination of weighted trees containing identical or overlapping sets of taxa. Syst. Biol. 46:306-312. (Pubitemid 127092068)
    • (1997) Systematic Biology , vol.46 , Issue.2 , pp. 306-312
    • Lapointe, F.-J.1    Cucumel, G.2
  • 38
    • 0033072060 scopus 로고    scopus 로고
    • Total Evidence, Consensus, and Bat Phylogeny: A Distance-Based Approach
    • DOI 10.1006/mpev.1998.0561, PII S1055790398905619
    • Lapointe, F.-J., J. A. W. Kirsch, and J. M. Hutcheon. 1999. Total evidence, consensus and bat phylogeny: A distance-based approach. Mol. Phylogenet. Evol. 11:55-66. (Pubitemid 129499252)
    • (1999) Molecular Phylogenetics and Evolution , vol.11 , Issue.1 , pp. 55-66
    • Lapointe, F.-J.1    Kirsch, J.A.W.2    Hutcheon, J.M.3
  • 39
    • 84864943965 scopus 로고    scopus 로고
    • A fast procedure for estimating missing distances in incomplete matrices prior to phylogenetic analysis. Pages
    • (N. El-Mabrouk, T. Lengauer, D. Sankoff, eds.). Publications CRM, Montréal
    • Lapointe, F.-J., and P.-A. Landry. 2001. A fast procedure for estimating missing distances in incomplete matrices prior to phylogenetic analysis. Pages 189-190 in Currents computational molecular biology (N. El-Mabrouk, T. Lengauer, D. Sankoff, eds.). Publications CRM, Montréal.
    • (2001) Currents Computational Molecular Biology , pp. 189-190
    • Lapointe, F.-J.1    Landry, P.-A.2
  • 40
    • 7444246349 scopus 로고    scopus 로고
    • Everything you always wanted to know about the average consensus, and more
    • (O. R. P. Bininda-Emonds, ed.). Kluwer Academic, Dordrecht
    • Lapointe, F.-J., and C. Levasseur. 2004. Everything you always wanted to know about the average consensus, and more. Pages 87-105 in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.). Kluwer Academic, Dordrecht.
    • (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life , pp. 87-105
    • Lapointe, F.-J.1    Levasseur, C.2
  • 41
    • 1642446507 scopus 로고    scopus 로고
    • Matrix Representations with Parsimony or with Distances: Two Sides of the Same Coin?
    • DOI 10.1080/10635150390252297
    • Lapointe, F.-J., M. Wilkinson, and D. Bryant. 2003. Matrix representation with parsimony or with distances: Two sides of the same coin? Syst. Biol. 52:865-868. (Pubitemid 38106054)
    • (2003) Systematic Biology , vol.52 , Issue.6 , pp. 865-868
    • Lapointe, F.-J.1    Wilkinson, M.2    Bryant, D.3
  • 42
    • 0035527394 scopus 로고    scopus 로고
    • War and peace in phylogenetics: A rejoinder on total evidence and consensus
    • Levasseur, C, and F.-J. Lapointe. 2001. War and peace in phylogenetics: A rejoinder on total evidence and consensus. Syst. Biol. 50:881-891.
    • (2001) Syst. Biol. , vol.50 , pp. 881-891
    • Levasseur, C.1    Lapointe, F.-J.2
  • 45
    • 2942528120 scopus 로고    scopus 로고
    • A molecular supertree of the Artiodactyla
    • (O. R. P. Bininda-Emonds, ed.). Kluwer Academic, Dordrecht
    • Mahon, S. A. 2004. A molecular supertree of the Artiodactyla. Pages 411-437 in Phylogenetic supertrees: Combining information to reveal the tree of life (O. R. P. Bininda-Emonds, ed.). Kluwer Academic, Dordrecht.
    • (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life , pp. 411-437
    • Mahon, S.A.1
  • 46
    • 0034894308 scopus 로고    scopus 로고
    • T-REX: Reconstructing and visualizing phylogenetic trees and reticulation networks
    • Makarenkov, V. 2001. TREX: Reconstructing and visualizing phylogenetic trees and reticulation networks. Bioinformatics 17:664-668. (Pubitemid 32707593)
    • (2001) Bioinformatics , vol.17 , Issue.7 , pp. 664-668
    • Makarenkov, V.1
  • 47
    • 4544263561 scopus 로고    scopus 로고
    • A weighted least-squares approach for inferring phylogenies from incomplete distance matrices
    • DOI 10.1093/bioinformatics/bth211
    • Makarenkov, V., and F.-J. Lapointe. 2004. A weighted least-squares approach for inferring phylogenies from incomplete distance matrices. Bioinformatics 20:2113-2121. (Pubitemid 39236564)
    • (2004) Bioinformatics , vol.20 , Issue.13 , pp. 2113-2121
    • Makarenkov, V.1    Lapointe, F.-J.2
  • 48
    • 0033243629 scopus 로고    scopus 로고
    • An algorithm for the fitting of a phylogenetic tree according to a weighted least-squares criterion
    • Makarenkov, V., and B. Leclerc. 1999. An algorithm for the fitting of a phylogenetic tree according to a weighted least-squares criterion. J. Classif. 16:3-26.
    • (1999) J. Classif. , vol.16 , pp. 3-26
    • Makarenkov, V.1    Leclerc, B.2
  • 49
    • 0024658495 scopus 로고
    • Variances of the average numbers of nucleotides substitutions within and between populations
    • Nei, M., and L. Jin. 1989. Variances of the average numbers of nucleotides substitutions within and between populations. Mol. Biol. Evol. 6:290-300.
    • (1989) Mol. Biol. Evol. , vol.6 , pp. 290-300
    • Nei, M.1    Jin, L.2
  • 50
    • 84956992917 scopus 로고    scopus 로고
    • Modified mincut supertrees
    • R. Guigo and D. Gusfield, eds.
    • Page, R. 2002. Modified mincut supertrees. Pages 537-552 in Lecture notes in computer science volume 2452 (R. Guigo and D. Gusfield, eds.).
    • (2002) Lecture Notes in Computer Science , vol.2452 , pp. 537-552
    • Page, R.1
  • 51
    • 17744386162 scopus 로고    scopus 로고
    • Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and protostomia
    • DOI 10.1093/molbev/msi111
    • Philippe, H., N. Lartillot, and H. Brinkmann. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22:1246-1253. (Pubitemid 40577762)
    • (2005) Molecular Biology and Evolution , vol.22 , Issue.5 , pp. 1246-1253
    • Philippe, H.1    Lartillot, N.2    Brinkmann, H.3
  • 54
    • 23144461098 scopus 로고    scopus 로고
    • A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla)
    • Price, S. A., O. R. P. Bininda-Emonds, and J. L. Gittleman. 2005. A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla). Biol. Rev. Comb. Philos. Soc. 80:445- 473.
    • (2005) Biol. Rev. Comb. Philos. Soc. , vol.80 , pp. 445-473
    • Price, S.A.1    Bininda-Emonds, O.R.P.2    Gittleman, J.L.3
  • 55
    • 0036900111 scopus 로고    scopus 로고
    • Combining multiple data sets in a likelihood analysis: Which models are the best?
    • Pupko, T, D. Huchon, Y. Cao, N. Okada, and M. Hasegawa. 2002. Combining multiple data sets in a likelihood analysis: Which models are the best? Mol. Biol. Evol. 19:2294-2307. (Pubitemid 35440463)
    • (2002) Molecular Biology and Evolution , vol.19 , Issue.12 , pp. 2294-2307
    • Pupko, T.1    Huchon, D.2    Cao, Y.3    Okada, N.4    Hasegawa, M.5
  • 56
    • 0026822436 scopus 로고
    • Phylogenetic inference based on matrix representation of trees
    • Ragan, M. A. 1992. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1:53-58.
    • (1992) Mol. Phylogenet. Evol. , vol.1 , pp. 53-58
    • Ragan, M.A.1
  • 57
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., and N. C. Grassly. 1997. SEQ-GEN: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp. Appl. Biosi. 13:235-238. (Pubitemid 27249927)
    • (1997) Computer Applications in the Biosciences , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 58
    • 0039348203 scopus 로고
    • Comparison of weighted labeled trees
    • Robinson, D., and L. Foulds. 1979. Comparison of weighted labeled trees. Lect. Notes Math. 748:119-126.
    • (1979) Lect. Notes Math. , vol.748 , pp. 119-126
    • Robinson, D.1    Foulds, L.2
  • 60
    • 0030311386 scopus 로고    scopus 로고
    • Matrix representation of trees, redundancy, and weighting
    • Ronquist, F. 1996. Matrix representation of trees, redundancy, and weighting. Syst. Biol. 45:247-253.
    • (1996) Syst. Biol. , vol.45 , pp. 247-253
    • Ronquist, F.1
  • 61
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., and M. Nei. 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
  • 62
    • 0037314098 scopus 로고    scopus 로고
    • r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • DOI 10.1093/bioinformatics/19.2.301
    • Sanderson, M. J. 2003. Inferring absolute rates of molecular evolution and divergence times in the absence of molecular clock. Bioinformatics 19:301-302. (Pubitemid 36181923)
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 301-302
    • Sanderson, M.J.1
  • 64
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504. (Pubitemid 34284960)
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 65
    • 0001541744 scopus 로고    scopus 로고
    • A supertree method for rooted trees
    • Semple, C, and M. Steel. 2000. A supertree method for rooted trees. Disc. Appl. Math. 105:147-158.
    • (2000) Disc. Appl. Math. , vol.105 , pp. 147-158
    • Semple, C.1    Steel, M.2
  • 66
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • DOI 10.1080/10635150290069913
    • Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508. (Pubitemid 35180700)
    • (2002) Systematic Biology , vol.51 , Issue.3 , pp. 492-508
    • Shimodaira, H.1
  • 67
    • 12044252586 scopus 로고
    • Distribution of tree comparison metrics - Some new results
    • Steel, M. A., and D. Penny. 1993. Distribution of tree comparison metrics - Some new results. Syst. Biol. 42:126-141.
    • (1993) Syst. Biol. , vol.42 , pp. 126-141
    • Steel, M.A.1    Penny, D.2
  • 68
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
    • Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969. (Pubitemid 26284912)
    • (1996) Molecular Biology and Evolution , vol.13 , Issue.7 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 69
    • 0024114801 scopus 로고
    • A note on the neighbor-joining method of Saitou and Nei
    • Studier, J. A., and K. J. Keppler. 1988. A note on the neighbor-joining method of Saitou and Nei. Mol. Biol. Evol. 5:729-731.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 729-731
    • Studier, J.A.1    Keppler, K.J.2
  • 71
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachussetts
    • Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. HiUis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachussetts.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    HiUis, D.M.4
  • 72
    • 0142089657 scopus 로고    scopus 로고
    • Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data
    • Waddell, P. J., H. Kishino, and R. Ota. 2002. Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data. Genome Inform. 13:82-92.
    • (2002) Genome Inform. , vol.13 , pp. 82-92
    • Waddell, P.J.1    Kishino, H.2    Ota, R.3
  • 73
    • 0141609706 scopus 로고    scopus 로고
    • Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models
    • DOI 10.1016/S1055-7903(03)00115-5
    • Waddell, P. J., and S. Shelley. 2003. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibriogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 28:197-224. (Pubitemid 37435989)
    • (2003) Molecular Phylogenetics and Evolution , vol.28 , Issue.2 , pp. 197-224
    • Waddell, P.J.1    Shelley, S.2
  • 74
    • 0032225748 scopus 로고    scopus 로고
    • Does adding characters with missing data increase or decrease phylogenetic accuracy?
    • Wiens, J. J. 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47:625-640. (Pubitemid 128370902)
    • (1998) Systematic Biology , vol.47 , Issue.4 , pp. 625-640
    • Wiens, J.J.1
  • 75
    • 0029466830 scopus 로고
    • Combining Data Sets with Different Numbers of Taxa for Phylogenetic Analysis
    • Wiens, J. J., and T. W. Reeder. 1995. Combining data sets with different numbers of taxa for phylogenetic analysis. Syst. Biol. 44:548-558. (Pubitemid 126021228)
    • (1995) Systematic Biology , vol.44 , Issue.4 , pp. 548-558
    • Wiens, J.J.1    Reeder, T.W.2
  • 76
    • 0029970097 scopus 로고    scopus 로고
    • Maximum-likelihood models for combined analyses of multiple sequence data
    • DOI 10.1007/BF02352289
    • Yang, Z. 1996. Maximum-likelihood models for combined analysis of multiple sequence data. J. Mol. Evol. 42:587-596. (Pubitemid 26197149)
    • (1996) Journal of Molecular Evolution , vol.42 , Issue.5 , pp. 587-596
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.