-
1
-
-
0002367729
-
-
Institute of Statistical Mathematics, Tokyo
-
Adachi J., and Hasegawa M. MOLPHY Version 2.3: Programs for Molecular Phylogenetics Based on Maximum Likelihood. Computer Science Monographs vol. 28 (1996), Institute of Statistical Mathematics, Tokyo 1-150
-
(1996)
Computer Science Monographs
, vol.28
, pp. 1-150
-
-
Adachi, J.1
Hasegawa, M.2
-
2
-
-
0002844544
-
Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
-
Baum B. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41 (2002) 3-10
-
(2002)
Taxon
, vol.41
, pp. 3-10
-
-
Baum, B.1
-
3
-
-
33744973813
-
Fast computation of supertrees for compatible phylogenies with nested taxa
-
Berry V., and Semple C. Fast computation of supertrees for compatible phylogenies with nested taxa. Syst. Biol. 55 (2006) 270-288
-
(2006)
Syst. Biol.
, vol.55
, pp. 270-288
-
-
Berry, V.1
Semple, C.2
-
6
-
-
19944417239
-
Supertree construction in the genomic age
-
Bininda-Emonds O.R.P. Supertree construction in the genomic age. Methods Enzymol. 395 (2005) 745-757
-
(2005)
Methods Enzymol.
, vol.395
, pp. 745-757
-
-
Bininda-Emonds, O.R.P.1
-
8
-
-
33846799228
-
Variation in evolutionary processes at different codon positions
-
Bofkin L., and Goldman N. Variation in evolutionary processes at different codon positions. Mol. Biol. Evol. 24 (2007) 513-521
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 513-521
-
-
Bofkin, L.1
Goldman, N.2
-
9
-
-
0035527383
-
Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support
-
Buckley T.R., Simon C., and Chambers G.K. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst. Biol. 50 (2001) 67-86
-
(2001)
Syst. Biol.
, vol.50
, pp. 67-86
-
-
Buckley, T.R.1
Simon, C.2
Chambers, G.K.3
-
10
-
-
33747375683
-
Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets
-
Burleigh J.G., Driskell A.C., and Sanderson M.J. Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Syst. Biol. 55 (2006) 426-440
-
(2006)
Syst. Biol.
, vol.55
, pp. 426-440
-
-
Burleigh, J.G.1
Driskell, A.C.2
Sanderson, M.J.3
-
11
-
-
13844250623
-
Clann: investigating phylogenetic information through supertree analyses
-
Creevey C.J., and McInerney J.O. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21 (2005) 390-392
-
(2005)
Bioinformatics
, vol.21
, pp. 390-392
-
-
Creevey, C.J.1
McInerney, J.O.2
-
12
-
-
34447341925
-
SDM: a fast distance-based approach for (super) tree building in phylogenomics
-
Criscuolo A., Berry V., Douzery E.J., and Gascuel O. SDM: a fast distance-based approach for (super) tree building in phylogenomics. Syst. Biol. 55 (2006) 740-755
-
(2006)
Syst. Biol.
, vol.55
, pp. 740-755
-
-
Criscuolo, A.1
Berry, V.2
Douzery, E.J.3
Gascuel, O.4
-
13
-
-
33845627286
-
The supermatrix approach to systematics
-
de Queiroz A., and Gatesy J. The supermatrix approach to systematics. Trends Ecol. Evol. 22 (2007) 34-41
-
(2007)
Trends Ecol. Evol.
, vol.22
, pp. 34-41
-
-
de Queiroz, A.1
Gatesy, J.2
-
15
-
-
0004128472
-
-
John Hopkins University Press, London
-
Edwards A.W.F. Likelihood (1992), John Hopkins University Press, London
-
(1992)
Likelihood
-
-
Edwards, A.W.F.1
-
16
-
-
2442598026
-
Performance of flip supertree construction with a heuristic algorithm
-
Eulenstein O., et al. Performance of flip supertree construction with a heuristic algorithm. Syst. Biol. 53 (2004) 299-308
-
(2004)
Syst. Biol.
, vol.53
, pp. 299-308
-
-
Eulenstein, O.1
-
17
-
-
0019797407
-
Evolutionary trees from DNA sequences: a maximum likelihood approach
-
Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
-
(1981)
J. Mol. Evol.
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
18
-
-
0034818755
-
Taking variation of evolutionary rates between sites into account in inferring phylogenies
-
Felsenstein J. Taking variation of evolutionary rates between sites into account in inferring phylogenies. J. Mol. Evol. 53 (2001) 447-455
-
(2001)
J. Mol. Evol.
, vol.53
, pp. 447-455
-
-
Felsenstein, J.1
-
19
-
-
0003991673
-
-
Sinauer Associates, Sunderland, Massachusetts
-
Felsenstein J. Inferring Phylogenies (2004), Sinauer Associates, Sunderland, Massachusetts
-
(2004)
Inferring Phylogenies
-
-
Felsenstein, J.1
-
21
-
-
2442449251
-
Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia
-
Gatesy J., Baker R.H., and Hayashi C. Inconsistencies in arguments for the supertree approach: supermatrices versus supertrees of Crocodylia. Syst. Biol. 53 (2004) 342-355
-
(2004)
Syst. Biol.
, vol.53
, pp. 342-355
-
-
Gatesy, J.1
Baker, R.H.2
Hayashi, C.3
-
22
-
-
27544472307
-
Minority rule supertrees? MRP, compatibility, and minimum flip may display the least frequent groups
-
Goloboff P.A. Minority rule supertrees? MRP, compatibility, and minimum flip may display the least frequent groups. Cladistics 21 (2005) 282-294
-
(2005)
Cladistics
, vol.21
, pp. 282-294
-
-
Goloboff, P.A.1
-
23
-
-
0036821385
-
Semi-strict supertrees
-
Goloboff P.A., and Pol D. Semi-strict supertrees. Cladistics 18 (2002) 514-525
-
(2002)
Cladistics
, vol.18
, pp. 514-525
-
-
Goloboff, P.A.1
Pol, D.2
-
24
-
-
0032023889
-
Taxonomic sampling, phylogenetic accuracy, and investigator bias
-
Hillis D.M. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47 (1998) 3-8
-
(1998)
Syst. Biol.
, vol.47
, pp. 3-8
-
-
Hillis, D.M.1
-
25
-
-
0029113744
-
The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
-
Huelsenbeck J.P. The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol. Biol. Evol. 12 (1995) 843-849
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 843-849
-
-
Huelsenbeck, J.P.1
-
27
-
-
0032746022
-
Disk-covering, a fast-converging method for phylogenetic tree reconstruction
-
Huson D.H., Nettles S.M., and Warnow T.J. Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6 (1999) 369-386
-
(1999)
J. Comput. Biol.
, vol.6
, pp. 369-386
-
-
Huson, D.H.1
Nettles, S.M.2
Warnow, T.J.3
-
28
-
-
0019296687
-
A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences
-
Kimura M. A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
-
(1980)
J. Mol. Evol.
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
29
-
-
0028177080
-
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates (Erratum in Mol. Biol. Evol. 1995; 12:525)
-
Kuhner M.K., and Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates (Erratum in Mol. Biol. Evol. 1995; 12:525). Mol. Biol. Evol. 11 (1994) 459-468
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 459-468
-
-
Kuhner, M.K.1
Felsenstein, J.2
-
31
-
-
33751227478
-
Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping
-
Moore B.R., Smith S.A., and Donoghue M.J. Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping. Syst. Biol. 55 (2006) 662-676
-
(2006)
Syst. Biol.
, vol.55
, pp. 662-676
-
-
Moore, B.R.1
Smith, S.A.2
Donoghue, M.J.3
-
32
-
-
39749188544
-
Rooting the Eutherian tree - the power and pitfalls of phylogenomics
-
Nishihara H., Okada N., and Hasegawa M. Rooting the Eutherian tree - the power and pitfalls of phylogenomics. Genome Biol. 8 (2007) R199
-
(2007)
Genome Biol.
, vol.8
-
-
Nishihara, H.1
Okada, N.2
Hasegawa, M.3
-
34
-
-
17744386162
-
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia
-
Philippe H., Lartillot N., and Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22 (2005) 1246-1253
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1246-1253
-
-
Philippe, H.1
Lartillot, N.2
Brinkmann, H.3
-
35
-
-
0036005524
-
MRP, taxonomic congruence and total evidence
-
Pisani D., and Wilkinson M. MRP, taxonomic congruence and total evidence. Syst. Biol. 51 (2002) 151-155
-
(2002)
Syst. Biol.
, vol.51
, pp. 151-155
-
-
Pisani, D.1
Wilkinson, M.2
-
36
-
-
0033602474
-
Taxon sampling revisited
-
Poe S., and Swofford D.L. Taxon sampling revisited. Nature 398 (1999) 299-300
-
(1999)
Nature
, vol.398
, pp. 299-300
-
-
Poe, S.1
Swofford, D.L.2
-
37
-
-
0036699885
-
Increased taxon sampling is advantageous for phylogenetic inference
-
Pollock D.D., Zwickl D.J., McGuire J.A., and Hillis D.M. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51 (2002) 664-671
-
(2002)
Syst. Biol.
, vol.51
, pp. 664-671
-
-
Pollock, D.D.1
Zwickl, D.J.2
McGuire, J.A.3
Hillis, D.M.4
-
38
-
-
0036900111
-
Combining multiple data sets in a likelihood analysis: which models are the best?
-
Pupko T., et al. Combining multiple data sets in a likelihood analysis: which models are the best?. Mol. Biol. Evol. 19 (2002) 2294-2307
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 2294-2307
-
-
Pupko, T.1
-
39
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
Ragan M.A. Phylogenetic inference based on matrix representation of trees. Mol. Phylogenet. Evol. 1 (1992) 53-58
-
(1992)
Mol. Phylogenet. Evol.
, vol.1
, pp. 53-58
-
-
Ragan, M.A.1
-
42
-
-
31344433677
-
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction
-
Ren F., Tanaka H., and Yang Z. An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst. Biol. 54 (2005) 808-818
-
(2005)
Syst. Biol.
, vol.54
, pp. 808-818
-
-
Ren, F.1
Tanaka, H.2
Yang, Z.3
-
43
-
-
2942556037
-
Bayesian supertree
-
Bininda-Emonds O.R.P. (Ed), Kluwer Academic, Dordrecht, the Netherlands
-
Ronquist F., Huelsenbeck J.P., and Britton T. Bayesian supertree. In: Bininda-Emonds O.R.P. (Ed). Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (2004), Kluwer Academic, Dordrecht, the Netherlands 193-224
-
(2004)
Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life
, pp. 193-224
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
Britton, T.3
-
44
-
-
0037291976
-
Taxon sampling, bioinformatics, and phylogenomics
-
Rosenberg M.S., and Kumar S. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52 (2003) 119-124
-
(2003)
Syst. Biol.
, vol.52
, pp. 119-124
-
-
Rosenberg, M.S.1
Kumar, S.2
-
45
-
-
0032030505
-
Phylogenetic supertrees: assembling the trees of life
-
Sanderson M.J. Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 13 (1998) 105-109
-
(1998)
Trends Ecol. Evol.
, vol.13
, pp. 105-109
-
-
Sanderson, M.J.1
-
46
-
-
0038158155
-
Obtaining maximal concatenated phylogenetic data sets from large sequence databases
-
Sanderson M.J., et al. Obtaining maximal concatenated phylogenetic data sets from large sequence databases. Mol. Biol. Evol. 20 (2003) 1036-1042
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1036-1042
-
-
Sanderson, M.J.1
-
47
-
-
0001541744
-
A supertree method for rooted trees
-
Semple C., and Steel M. A supertree method for rooted trees. Discrete Appl. Math. 105 (2000) 147-158
-
(2000)
Discrete Appl. Math.
, vol.105
, pp. 147-158
-
-
Semple, C.1
Steel, M.2
-
48
-
-
28944450584
-
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
-
Shapiro B., Rambaut A., and Drummond A.J. Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol. 23 (2006) 7-9
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 7-9
-
-
Shapiro, B.1
Rambaut, A.2
Drummond, A.J.3
-
49
-
-
33845385936
-
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA
-
Simon C., et al. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 37 (2006) 545-579
-
(2006)
Annu. Rev. Ecol. Evol. Syst.
, vol.37
, pp. 545-579
-
-
Simon, C.1
-
50
-
-
0035793899
-
Phylogenetics. Which mammalian supertree to bark up?
-
Springer M.S., and de Jong W.W. Phylogenetics. Which mammalian supertree to bark up?. Science 291 (2001) 1709-1711
-
(2001)
Science
, vol.291
, pp. 1709-1711
-
-
Springer, M.S.1
de Jong, W.W.2
-
51
-
-
0242404116
-
Hierarchical phylogenetic models for analyzing multipartite sequence data
-
Suchard M.A., Kitchen C.M., Sinsheimer J.S., and Weiss R.E. Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst. Biol. 52 (2003) 649-664
-
(2003)
Syst. Biol.
, vol.52
, pp. 649-664
-
-
Suchard, M.A.1
Kitchen, C.M.2
Sinsheimer, J.S.3
Weiss, R.E.4
-
52
-
-
0028205953
-
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
-
Tateno Y., Takezaki N., and Nei M. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol. Biol. Evol. 11 (1994) 261-277
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 261-277
-
-
Tateno, Y.1
Takezaki, N.2
Nei, M.3
-
53
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne J.L., Kishino H., and Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15 (1998) 1647-1657
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 1647-1657
-
-
Thorne, J.L.1
Kishino, H.2
Painter, I.S.3
-
54
-
-
30344464074
-
Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?
-
Wiens J.J. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?. Syst. Biol. 54 (2005) 731-742
-
(2005)
Syst. Biol.
, vol.54
, pp. 731-742
-
-
Wiens, J.J.1
-
55
-
-
22844442070
-
The shape of supertrees to come: tree shape related properties of fourteen supertree methods
-
Wilkinson M., et al. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst. Biol. 54 (2005) 419-431
-
(2005)
Syst. Biol.
, vol.54
, pp. 419-431
-
-
Wilkinson, M.1
-
56
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
-
Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39 (1994) 306-314
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
57
-
-
0029067458
-
Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
-
Yang Z. Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites. J. Mol. Evol. 40 (1995) 689-697
-
(1995)
J. Mol. Evol.
, vol.40
, pp. 689-697
-
-
Yang, Z.1
-
58
-
-
0029970097
-
Maximum-likelihood models for combined analyses of multiple sequence data
-
Yang Z. Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42 (1996) 587-596
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 587-596
-
-
Yang, Z.1
-
59
-
-
0030683599
-
PAML: a program package for phylogenetic analysis by maximum likelihood
-
Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
60
-
-
20144385989
-
A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times
-
Yang Z. A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times. Acta Zoologica Sinica 50 (2004) 645-656
-
(2004)
Acta Zoologica Sinica
, vol.50
, pp. 645-656
-
-
Yang, Z.1
-
62
-
-
28944451210
-
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
-
Yang Z., and Rannala B. Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol. Biol. Evol. 23 (2006) 212-226
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 212-226
-
-
Yang, Z.1
Rannala, B.2
-
63
-
-
0036699481
-
Increased taxon sampling greatly reduces phylogenetic error
-
Zwickl D.J., and Hillis D.M. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51 (2002) 588-598
-
(2002)
Syst. Biol.
, vol.51
, pp. 588-598
-
-
Zwickl, D.J.1
Hillis, D.M.2
|