-
2
-
-
0014754463
-
Genetic transfer and bacterial taxonomy
-
Jones, D., Sneath, P. H. A. (1970) Genetic transfer and bacterial taxonomy. Bacteriological Rev 34, 40-81.
-
(1970)
Bacteriological Rev
, vol.34
, pp. 40-81
-
-
Jones, D.1
Sneath, P.H.A.2
-
3
-
-
0026332291
-
Evidence for horizontal transfer in Escherichia coli speciation
-
Medigue, C., Rouxel, T., Vigier, P., et al. (1991) Evidence for horizontal transfer in Escherichia coli speciation. J Mol Biol 222, 851-856.
-
(1991)
J Mol Biol
, vol.222
, pp. 851-856
-
-
Medigue, C.1
Rouxel, T.2
Vigier, P.3
-
4
-
-
26444506791
-
Highways of gene sharing in prokaryotes
-
Beiko, R. G., Harlow, T. J., Ragan, M. A. (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A 102, 14332-14337.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 14332-14337
-
-
Beiko, R.G.1
Harlow, T.J.2
Ragan, M.A.3
-
5
-
-
0033616714
-
Horizontal gene transfer among genomes: The complexity hypothesis
-
Jain, R., Rivera, M. C., Lake, J. A. (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A 96, 3801-3806.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 3801-3806
-
-
Jain, R.1
Rivera, M.C.2
Lake, J.A.3
-
6
-
-
10944251626
-
Genome phylogenies
-
Hirt, R. P, Horne, D. S, eds, CRC Press, Boca Raton, FL
-
Charlebois, R. L., Beiko, R. G., Ragan, M. A. (2004) Genome phylogenies, in (Hirt, R. P., Horne, D. S., eds.), Organelles Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics. CRC Press, Boca Raton, FL.
-
(2004)
Organelles Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics
-
-
Charlebois, R.L.1
Beiko, R.G.2
Ragan, M.A.3
-
7
-
-
0032568375
-
The complete genome of the hyperthermophilic bacterium Aquifex aeolicus
-
Deckert, G., Warren, P. V., Gaasterland, T., et al. (1998) The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392, 353-358.
-
(1998)
Nature
, vol.392
, pp. 353-358
-
-
Deckert, G.1
Warren, P.V.2
Gaasterland, T.3
-
8
-
-
0033609333
-
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
-
Nelson, K. E., Clayton, R. A., Gill, S. R., et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323-329.
-
(1999)
Nature
, vol.399
, pp. 323-329
-
-
Nelson, K.E.1
Clayton, R.A.2
Gill, S.R.3
-
9
-
-
0035943134
-
On surrogate methods for detecting lateral gene transfer
-
Ragan, M. A. (2001) On surrogate methods for detecting lateral gene transfer. FEMS Microbiol Lett 201, 187-191.
-
(2001)
FEMS Microbiol Lett
, vol.201
, pp. 187-191
-
-
Ragan, M.A.1
-
10
-
-
30344471824
-
Do different surrogate methods detect lateral genetic transfer events of different relative ages?
-
Ragan, M. A., Harlow, T. J., Beiko, R. G. (2006) Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends Microbiol 14, 4-8.
-
(2006)
Trends Microbiol
, vol.14
, pp. 4-8
-
-
Ragan, M.A.1
Harlow, T.J.2
Beiko, R.G.3
-
11
-
-
4644252702
-
Tracing the decay of the historical signal in biological sequence data
-
Ho, S. Y., Jermiin, L. (2004) Tracing the decay of the historical signal in biological sequence data. Syst Biol 53, 623-637.
-
(2004)
Syst Biol
, vol.53
, pp. 623-637
-
-
Ho, S.Y.1
Jermiin, L.2
-
12
-
-
4644299089
-
The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
-
Jermiin, L., Ho, S. Y., Ababneh, F., et al. (2004) The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst Biol 53, 638-643.
-
(2004)
Syst Biol
, vol.53
, pp. 638-643
-
-
Jermiin, L.1
Ho, S.Y.2
Ababneh, F.3
-
13
-
-
0042902833
-
The COG database: An updated version includes eukaryotes
-
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 41
-
-
Tatusov, R.L.1
Fedorova, N.D.2
Jackson, J.D.3
-
14
-
-
0035166979
-
The comprehensive microbial resource
-
Peterson, J. D., Umayam, L. A., Dickinson, T., et al. (2001) The comprehensive microbial resource. Nucleic Acids Res 29, 123-125.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 123-125
-
-
Peterson, J.D.1
Umayam, L.A.2
Dickinson, T.3
-
16
-
-
0031684427
-
Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm
-
Rigoutsos, I., Floratos, A. (1998) Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 14, 55-67.
-
(1998)
Bioinformatics
, vol.14
, pp. 55-67
-
-
Rigoutsos, I.1
Floratos, A.2
-
17
-
-
19544381576
-
A word-oriented approach to alignment validation
-
Beiko, R. G., Chan, C. X., Ragan, M. A. (2005) A word-oriented approach to alignment validation. Bioinformatics 21, 2230-2239.
-
(2005)
Bioinformatics
, vol.21
, pp. 2230-2239
-
-
Beiko, R.G.1
Chan, C.X.2
Ragan, M.A.3
-
18
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J. D., Higgins, D. G., Gibson, T. J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
19
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame, C., Higgins, D. G., Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302, 205-217.
-
(2000)
J Mol Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
20
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
Lee, C., Grasso, C., Sharlow, M. F. (2002) Multiple sequence alignment using partial order graphs. Bioinformatics 18, 452-464.
-
(2002)
Bioinformatics
, vol.18
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
21
-
-
0030582739
-
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
-
Gotoh, O. (1996) Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 264, 823-838.
-
(1996)
J Mol Biol
, vol.264
, pp. 823-838
-
-
Gotoh, O.1
-
22
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh, K., Misawa, K., Kuma, K., et al. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30, 3059-3066.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
-
23
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck, J. P., Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
24
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540-552.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
25
-
-
13844250623
-
Clann: Investigating phylogenetic information through supertree analyses
-
Creevey, C. J., McInerney, J. O. (2005) Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21, 390-392.
-
(2005)
Bioinformatics
, vol.21
, pp. 390-392
-
-
Creevey, C.J.1
McInerney, J.O.2
-
26
-
-
33645568886
-
Phylogenetic identification of lateral genetic transfer events
-
Beiko, R. G., Hamilton, N. H. (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.H.2
-
27
-
-
0030801002
-
Gapped BLAST and PSIBLAST: A new generation of protein database search programs
-
Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
-
28
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., Westbrook, J., Feng, Z., et al. (2000) The Protein Data Bank. Nucleic Acids Res 28, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
-
29
-
-
2942513067
-
A hybrid clustering approach to recognition of protein families in 114 microbial genomes
-
Harlow, T. J., Gogarten, J. P., Ragan, M. A. (2004) A hybrid clustering approach to recognition of protein families in 114 microbial genomes. BMC Bioinformatics 5, 45.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 45
-
-
Harlow, T.J.1
Gogarten, J.P.2
Ragan, M.A.3
-
31
-
-
0031350056
-
NEXUS: An extensible file format for systematic information
-
Maddison, D. R., Swofford, D. L., Maddison, W. P. (1997) NEXUS: an extensible file format for systematic information. Syst Biol 46, 590-621.
-
(1997)
Syst Biol
, vol.46
, pp. 590-621
-
-
Maddison, D.R.1
Swofford, D.L.2
Maddison, W.P.3
-
32
-
-
33846141299
-
Searching for convergence in Markov chain Monte Carlo
-
Beiko, R. G., Keith, J. M., Harlow, T. J., Ragan, M.A. (2006) Searching for convergence in Markov chain Monte Carlo. Syst Biol. 55, 553-565.
-
(2006)
Syst Biol
, vol.55
, pp. 553-565
-
-
Beiko, R.G.1
Keith, J.M.2
Harlow, T.J.3
Ragan, M.A.4
-
33
-
-
0002844544
-
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
-
34
-
-
0026822436
-
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
-
35
-
-
84972511893
-
Practical Markov chain Monte Carlo
-
Geyer, C. J. (1992) Practical Markov chain Monte Carlo. Stat Sci 7, 473-483.
-
(1992)
Stat Sci
, vol.7
, pp. 473-483
-
-
Geyer, C.J.1
-
36
-
-
0030539336
-
Markov chain Monte Carlo convergence diagnostics: A comparative review
-
Cowles, M. K., Carlin, B. P. (1996) Markov chain Monte Carlo convergence diagnostics: a comparative review. J Amer Statist Assoc 91, 883-904.
-
(1996)
J Amer Statist Assoc
, vol.91
, pp. 883-904
-
-
Cowles, M.K.1
Carlin, B.P.2
-
38
-
-
22844442070
-
The shape of supertrees to come: Tree shape related properties of fourteen supertree methods
-
Wilkinson, M., Cotton, J. A., Creevey, C., et al. (2005) The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol 54, 419-431.
-
(2005)
Syst Biol
, vol.54
, pp. 419-431
-
-
Wilkinson, M.1
Cotton, J.A.2
Creevey, C.3
-
39
-
-
0037058983
-
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
-
Suzuki, Y., Glazko, G. V., Nei, M. (2002) Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc Natl Acad Sci U S A 99, 16138-16143.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 16138-16143
-
-
Suzuki, Y.1
Glazko, G.V.2
Nei, M.3
-
41
-
-
0025873313
-
Tracing origins with molecular sequences: Rooting the universal tree of life
-
Linkkila, T. P., Gogarten, J. P. (1991) Tracing origins with molecular sequences: rooting the universal tree of life. Trends Biochem Sci 16, 287-288.
-
(1991)
Trends Biochem Sci
, vol.16
, pp. 287-288
-
-
Linkkila, T.P.1
Gogarten, J.P.2
-
42
-
-
33645430074
-
Ancestral maximum likelihood of evolutionary trees is hard
-
Addario-Berry, L., Chor, B., Hallett, M., et al. (2003) Ancestral maximum likelihood of evolutionary trees is hard. Algorithms Bioinformat Proc 2812, 202-215.
-
(2003)
Algorithms Bioinformat Proc
, vol.2812
, pp. 202-215
-
-
Addario-Berry, L.1
Chor, B.2
Hallett, M.3
-
43
-
-
18944369385
-
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
-
MacLeod, D., Charlebois, R. L., Doolittle, F., et al. (2005) Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol Biol 5, 27.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 27
-
-
MacLeod, D.1
Charlebois, R.L.2
Doolittle, F.3
-
44
-
-
0028177080
-
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
-
Kuhner, M. K., 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
-
45
-
-
11944268967
-
Performance of phylogenetic methods in simulation
-
Huelsenbeck, J. P. (1995) Performance of phylogenetic methods in simulation. Syst Biol 44, 17-48.
-
(1995)
Syst Biol
, vol.44
, pp. 17-48
-
-
Huelsenbeck, J.P.1
-
46
-
-
0031297695
-
General time-reversible distances with unequal rates across sites: Mixing gamma and inverse Gaussian distributions with invariant sites
-
Waddell, P. J., Steel, M. A. (1997) General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. Mol Phylogenet Evol 8, 398-414.
-
(1997)
Mol Phylogenet Evol
, vol.8
, pp. 398-414
-
-
Waddell, P.J.1
Steel, M.A.2
-
47
-
-
0032927161
-
Topological bias and inconsistency of maximum likelihood using wrong models
-
Bruno, W. J., Halpern, A. L. (1999) Topological bias and inconsistency of maximum likelihood using wrong models. Mol Biol Evol 16, 564-566.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 564-566
-
-
Bruno, W.J.1
Halpern, A.L.2
-
48
-
-
0242490943
-
Lateral gene transfer: When will adolescence end?
-
Lawrence, J. G., Hendrickson, H. (2003) Lateral gene transfer: when will adolescence end? Mol Microbiol 50, 739-749.
-
(2003)
Mol Microbiol
, vol.50
, pp. 739-749
-
-
Lawrence, J.G.1
Hendrickson, H.2
|