-
1
-
-
23944475626
-
Mechanisms of, and barriers to, horizontal gene transfer between bacteria
-
10.1038/nrmicro1234, 16138099
-
Thomas CM, Nielsen KM. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat Rev Microbiol 2005, 3(9):711-721. 10.1038/nrmicro1234, 16138099.
-
(2005)
Nat Rev Microbiol
, vol.3
, Issue.9
, pp. 711-721
-
-
Thomas, C.M.1
Nielsen, K.M.2
-
2
-
-
0027738868
-
Horizontal transfer of ATPase genes-the tree of life becomes a net of life
-
Hilario E, Gogarten JP. Horizontal transfer of ATPase genes-the tree of life becomes a net of life. Biosystems 1993, 31(2-3):111-119.
-
(1993)
Biosystems
, vol.31
, Issue.2-3
, pp. 111-119
-
-
Hilario, E.1
Gogarten, J.P.2
-
3
-
-
0032076051
-
Genome data shake tree of life
-
10.1126/science.280.5364.672, 9599142
-
Pennisi E. Genome data shake tree of life. Science 1998, 280(5364):672-674. 10.1126/science.280.5364.672, 9599142.
-
(1998)
Science
, vol.280
, Issue.5364
, pp. 672-674
-
-
Pennisi, E.1
-
4
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
10.1126/science.284.5423.2124, 10381871
-
Doolittle WF. Phylogenetic classification and the universal tree. Science 1999, 284(5423):2124-2129. 10.1126/science.284.5423.2124, 10381871.
-
(1999)
Science
, vol.284
, Issue.5423
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
5
-
-
33846659065
-
Importance of widespread gene transfer agent genes in alpha-proteobacteria
-
10.1016/j.tim.2006.12.001, 17184993
-
Lang AS, Beatty JT. Importance of widespread gene transfer agent genes in alpha-proteobacteria. Trends Microbiol 2007, 15(2):54-62. 10.1016/j.tim.2006.12.001, 17184993.
-
(2007)
Trends Microbiol
, vol.15
, Issue.2
, pp. 54-62
-
-
Lang, A.S.1
Beatty, J.T.2
-
6
-
-
77957355684
-
High frequency of horizontal gene transfer in the oceans
-
10.1126/science.1192243, 20929803
-
McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH. High frequency of horizontal gene transfer in the oceans. Science 2010, 330(6000):50. 10.1126/science.1192243, 20929803.
-
(2010)
Science
, vol.330
, Issue.6000
, pp. 50
-
-
McDaniel, L.D.1
Young, E.2
Delaney, J.3
Ruhnau, F.4
Ritchie, K.B.5
Paul, J.H.6
-
7
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005, 6(5):361-375.
-
(2005)
Nat Rev Genet
, vol.6
, Issue.5
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
8
-
-
0036931408
-
The (super)tree of life: procedures, problems, and prospects
-
Bininda-Emonds ORP, Gittleman JL, Steel MA. The (super)tree of life: procedures, problems, and prospects. Annu Rev Ecol Syst 2002, 33(1):265-289.
-
(2002)
Annu Rev Ecol Syst
, vol.33
, Issue.1
, pp. 265-289
-
-
Bininda-Emonds, O.R.P.1
Gittleman, J.L.2
Steel, M.A.3
-
9
-
-
0036061865
-
A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history
-
10.1101/gr.187002, 186629, 12097345
-
Daubin V, Gouy M, Perriere G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 2002, 12(7):1080-1090. 10.1101/gr.187002, 186629, 12097345.
-
(2002)
Genome Res
, vol.12
, Issue.7
, pp. 1080-1090
-
-
Daubin, V.1
Gouy, M.2
Perriere, G.3
-
10
-
-
0028891511
-
Use of spectral analysis to test hypotheses on the origin of pinnipeds
-
Lento GM, Hickson RE, Chambers GK, Penny D. Use of spectral analysis to test hypotheses on the origin of pinnipeds. Mol Biol Evol 1995, 12(1):28-52.
-
(1995)
Mol Biol Evol
, vol.12
, Issue.1
, pp. 28-52
-
-
Lento, G.M.1
Hickson, R.E.2
Chambers, G.K.3
Penny, D.4
-
11
-
-
1942422301
-
Genome mosaicism and organismal lineages
-
10.1016/j.tig.2004.03.009, 15109780
-
Zhaxybayeva O, Lapierre P, Gogarten JP. Genome mosaicism and organismal lineages. Trends Genet 2004, 20(5):254-260. 10.1016/j.tig.2004.03.009, 15109780.
-
(2004)
Trends Genet
, vol.20
, Issue.5
, pp. 254-260
-
-
Zhaxybayeva, O.1
Lapierre, P.2
Gogarten, J.P.3
-
12
-
-
34047234772
-
The power of phylogenetic approaches to detect horizontally transferred genes
-
10.1186/1471-2148-7-45, 1847511, 17376230
-
Poptsova MS, Gogarten JP. The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evol Biol 2007, 7(1):45. 10.1186/1471-2148-7-45, 1847511, 17376230.
-
(2007)
BMC Evol Biol
, vol.7
, Issue.1
, pp. 45
-
-
Poptsova, M.S.1
Gogarten, J.P.2
-
13
-
-
77149147828
-
Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus
-
Zhaxybayeva O, Doolittle WF, Papke RT, Gogarten JP. Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus. Genome Biol Evol 2009, 2009:325-339.
-
(2009)
Genome Biol Evol
, vol.2009
, pp. 325-339
-
-
Zhaxybayeva, O.1
Doolittle, W.F.2
Papke, R.T.3
Gogarten, J.P.4
-
14
-
-
33748277982
-
Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events
-
10.1101/gr.5322306, 1557764, 16899658
-
Zhaxybayeva O, Gogarten JP, Charlebois RL, Doolittle WF, Papke RT. Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 2006, 16(9):1099-1108. 10.1101/gr.5322306, 1557764, 16899658.
-
(2006)
Genome Res
, vol.16
, Issue.9
, pp. 1099-1108
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
Charlebois, R.L.3
Doolittle, W.F.4
Papke, R.T.5
-
15
-
-
0031002417
-
Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment
-
10.1073/pnas.94.13.6815, 21241, 9192648
-
Strimmer K, von Haeseler A. Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci USA 1997, 94(13):6815-6819. 10.1073/pnas.94.13.6815, 21241, 9192648.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, Issue.13
, pp. 6815-6819
-
-
Strimmer, K.1
von Haeseler, A.2
-
16
-
-
0030928378
-
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A, Grassly NC. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 1997, 13(3):235-238.
-
(1997)
Comput Appl Biosci
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
17
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
10.1093/oxfordjournals.molbev.a003851, 11319253
-
Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18(5):691-699. 10.1093/oxfordjournals.molbev.a003851, 11319253.
-
(2001)
Mol Biol Evol
, vol.18
, Issue.5
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
19
-
-
77949718257
-
FastTree 2-approximately maximum-likelihood trees for large alignments
-
10.1371/journal.pone.0009490, 2835736, 20224823
-
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010, 5(3):e9490. 10.1371/journal.pone.0009490, 2835736, 20224823.
-
(2010)
PLoS One
, vol.5
, Issue.3
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
20
-
-
0029836454
-
Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies
-
Strimmer K, von Haeseler A. Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 1996, 13(7):964.
-
(1996)
Mol Biol Evol
, vol.13
, Issue.7
, pp. 964
-
-
Strimmer, K.1
von Haeseler, A.2
-
21
-
-
0036205377
-
Tree-puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing
-
10.1093/bioinformatics/18.3.502, 11934758
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A. Tree-puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18(3):502-504. 10.1093/bioinformatics/18.3.502, 11934758.
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
von Haeseler, A.4
-
22
-
-
13844250623
-
Clann: investigating phylogenetic information through supertree analyses
-
10.1093/bioinformatics/bti020, 15374874
-
Creevey CJ, McInerney JO. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 2005, 21(3):390-392. 10.1093/bioinformatics/bti020, 15374874.
-
(2005)
Bioinformatics
, vol.21
, Issue.3
, pp. 390-392
-
-
Creevey, C.J.1
McInerney, J.O.2
-
23
-
-
2442531708
-
Quartet Supertrees
-
Springer, Dordrecht, Bininda-Emonds ORP
-
Piaggio-Talice RB, Gordon, Eulenstein O. Quartet Supertrees. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life 2004, 173-192. Springer, Dordrecht, Bininda-Emonds ORP.
-
(2004)
Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life
, pp. 173-192
-
-
Piaggio-Talice, R.B.1
Gordon2
Eulenstein, O.3
-
24
-
-
9144255640
-
An improved probability mapping approach to assess genome mosaicism
-
10.1186/1471-2164-4-37, 222983, 12974984
-
Zhaxybayeva O, Gogarten JP. An improved probability mapping approach to assess genome mosaicism. BMC Genomics 2003, 4(1):37. 10.1186/1471-2164-4-37, 222983, 12974984.
-
(2003)
BMC Genomics
, vol.4
, Issue.1
, pp. 37
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
-
25
-
-
0030207565
-
Instability of quartet analyses of molecular sequence data by the maximum likelihood method: the Cetacea/Artiodactyla relationships
-
10.1006/mpev.1996.0059, 8812307
-
Adachi J, Hasegawa M. Instability of quartet analyses of molecular sequence data by the maximum likelihood method: the Cetacea/Artiodactyla relationships. Mol Phylogenet Evol 1996, 6(1):72-76. 10.1006/mpev.1996.0059, 8812307.
-
(1996)
Mol Phylogenet Evol
, vol.6
, Issue.1
, pp. 72-76
-
-
Adachi, J.1
Hasegawa, M.2
-
26
-
-
77649259858
-
Inferring and validating horizontal gene transfer events using bipartition dissimilarity
-
10.1093/sysbio/syp103, 20525630
-
Boc A, Philippe H, Makarenkov V. Inferring and validating horizontal gene transfer events using bipartition dissimilarity. Syst Biol 2010, 59(2):195-211. 10.1093/sysbio/syp103, 20525630.
-
(2010)
Syst Biol
, vol.59
, Issue.2
, pp. 195-211
-
-
Boc, A.1
Philippe, H.2
Makarenkov, V.3
-
27
-
-
79951935646
-
Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data
-
10.1371/journal.pone.0016751, 3040217, 21359176
-
Silver AC, Williams D, Faucher J, Horneman AJ, Gogarten JP, Graf J. Complex evolutionary history of the Aeromonas veronii group revealed by host interaction and DNA sequence data. PLoS One 2011, 6(2):e16751. 10.1371/journal.pone.0016751, 3040217, 21359176.
-
(2011)
PLoS One
, vol.6
, Issue.2
-
-
Silver, A.C.1
Williams, D.2
Faucher, J.3
Horneman, A.J.4
Gogarten, J.P.5
Graf, J.6
-
28
-
-
79955559191
-
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
-
10.1073/pnas.1015622108, 3084108, 21482770
-
Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT. Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species. Proc Natl Acad Sci USA 2011, 108(17):7200-7205. 10.1073/pnas.1015622108, 3084108, 21482770.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.17
, pp. 7200-7205
-
-
Luo, C.1
Walk, S.T.2
Gordon, D.M.3
Feldgarden, M.4
Tiedje, J.M.5
Konstantinidis, K.T.6
-
29
-
-
65249126970
-
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
-
10.1073/pnas.0901260106, 2667022, 19307556
-
Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM, DeBoy RT, Nelson KE, Nesbo CL, Doolittle WF, Gogarten JP, et al. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci USA 2009, 106(14):5865-5870. 10.1073/pnas.0901260106, 2667022, 19307556.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.14
, pp. 5865-5870
-
-
Zhaxybayeva, O.1
Swithers, K.S.2
Lapierre, P.3
Fournier, G.P.4
Bickhart, D.M.5
DeBoy, R.T.6
Nelson, K.E.7
Nesbo, C.L.8
Doolittle, W.F.9
Gogarten, J.P.10
-
30
-
-
79952201675
-
The tree and net components of prokaryote evolution
-
10.1093/gbe/evq062, 2997564, 20889655
-
Puigbò P, Wolf YI, Koonin EV. The tree and net components of prokaryote evolution. Genome Biol Evol 2010, 2:745-756. 10.1093/gbe/evq062, 2997564, 20889655.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 745-756
-
-
Puigbò, P.1
Wolf, Y.I.2
Koonin, E.V.3
-
31
-
-
18644368714
-
The bioperl toolkit: perl modules for the life sciences
-
10.1101/gr.361602, 187536, 12368254
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, et al. The bioperl toolkit: perl modules for the life sciences. Genome Res 2002, 12(10):1611-1618. 10.1101/gr.361602, 187536, 12368254.
-
(2002)
Genome Res
, vol.12
, Issue.10
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
Fuellen, G.7
Gilbert, J.G.R.8
Korf, I.9
Lapp, H.10
-
32
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson DH, Bryant D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 2006, 23(2):254-267.
-
(2006)
Mol Biol Evol
, vol.23
, Issue.2
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
33
-
-
80052097306
-
A rooted net of life
-
10.1186/1745-6150-6-45, 3189188, 21936906
-
Williams D, Fournier GP, Lapierre P, Swithers KS, Green AG, Andam CP, Gogarten JP. A rooted net of life. Biol Direct 2011, 6:45. 10.1186/1745-6150-6-45, 3189188, 21936906.
-
(2011)
Biol Direct
, vol.6
, pp. 45
-
-
Williams, D.1
Fournier, G.P.2
Lapierre, P.3
Swithers, K.S.4
Green, A.G.5
Andam, C.P.6
Gogarten, J.P.7
-
34
-
-
78651310799
-
Database resources of the National Center for Biotechnology Information
-
3013733, 21097890
-
Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2011, 39(Database issue):D38-D51. 3013733, 21097890.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.DATABASE ISSUE
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bolton, E.4
Bryant, S.H.5
Canese, K.6
Chetvernin, V.7
Church, D.M.8
DiCuccio, M.9
Federhen, S.10
-
35
-
-
23944499633
-
Horizontal gene transfer, genome innovation and evolution
-
10.1038/nrmicro1204, 16138096
-
Gogarten JP, Townsend JP. Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 2005, 3(9):679-687. 10.1038/nrmicro1204, 16138096.
-
(2005)
Nat Rev Microbiol
, vol.3
, Issue.9
, pp. 679-687
-
-
Gogarten, J.P.1
Townsend, J.P.2
-
36
-
-
12044253190
-
An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
-
Hillis DM, Bull JJ. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 1993, 42:182-192.
-
(1993)
Syst Biol
, vol.42
, pp. 182-192
-
-
Hillis, D.M.1
Bull, J.J.2
-
37
-
-
79959256644
-
Biased gene transfer in microbial evolution
-
10.1038/nrmicro2593, 21666709
-
Andam CP, Gogarten JP. Biased gene transfer in microbial evolution. Nat Rev Microbiol 2011, 9(7):543-555. 10.1038/nrmicro2593, 21666709.
-
(2011)
Nat Rev Microbiol
, vol.9
, Issue.7
, pp. 543-555
-
-
Andam, C.P.1
Gogarten, J.P.2
-
38
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 1978, 27(4):401-410.
-
(1978)
Syst Zool
, vol.27
, Issue.4
, pp. 401-410
-
-
Felsenstein, J.1
-
39
-
-
1542347067
-
Neighbor-net: an agglomerative method for the construction of phylogenetic networks
-
Bryant D, Moulton V. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 2004, 21(2):255-265.
-
(2004)
Mol Biol Evol
, vol.21
, Issue.2
, pp. 255-265
-
-
Bryant, D.1
Moulton, V.2
-
40
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
10.1016/1055-7903(92)90035-F, 1342924
-
Ragan MA. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol 1992, 1(1):53-58. 10.1016/1055-7903(92)90035-F, 1342924.
-
(1992)
Mol Phylogenet Evol
, vol.1
, Issue.1
, pp. 53-58
-
-
Ragan, M.A.1
-
41
-
-
0002844544
-
Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
-
Baum BR. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 1992, 41(1):3-10.
-
(1992)
Taxon
, vol.41
, Issue.1
, pp. 3-10
-
-
Baum, B.R.1
|