-
1
-
-
3042595153
-
Patterns of bacterial gene movement
-
10.1093/molbev/msh129. 15115802
-
Patterns of bacterial gene movement. W Hao BG Golding, Mol Biol Evol 2004 21 7 1294 1307 10.1093/molbev/msh129 15115802
-
(2004)
Mol Biol Evol
, vol.21
, Issue.7
, pp. 1294-1307
-
-
Hao, W.1
Golding, B.G.2
-
2
-
-
27144493223
-
Genome trees and the nature of genome evolution
-
10.1146/annurev.micro.59.030804.121233. 16153168
-
Genome trees and the nature of genome evolution. B Snel MA Huynen BE Dutilh, Annu Rev Microbiol 2005 59 191 209 10.1146/annurev.micro.59.030804. 121233 16153168
-
(2005)
Annu Rev Microbiol
, vol.59
, pp. 191-209
-
-
Snel, B.1
Huynen, M.A.2
Dutilh, B.E.3
-
3
-
-
34547830869
-
Reconstruction of highly heterogeneous gene-content evolution across the three domains of life
-
10.1093/bioinformatics/btm165. 17646301
-
Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. W Iwasaki T Takagi, Bioinformatics 2007 23 13 230 239 10.1093/bioinformatics/btm165 17646301
-
(2007)
Bioinformatics
, vol.23
, Issue.13
, pp. 9230-239
-
-
Iwasaki, W.1
Takagi, T.2
-
4
-
-
0036499057
-
SHOT: A web server for the construction of genome phylogenies
-
10.1016/S0168-9525(01)02597-5. 11858840
-
SHOT: a web server for the construction of genome phylogenies. JO Korbel B Snel MA Huynen P Bork, Trends Genet 2002 18 3 158 162 10.1016/S0168-9525(01) 02597-5 11858840
-
(2002)
Trends Genet
, vol.18
, Issue.3
, pp. 158-162
-
-
Korbel, J.O.1
Snel, B.2
Huynen, M.A.3
Bork, P.4
-
5
-
-
33847312769
-
Conditioned genome reconstruction: How to avoid choosing the conditioning genome
-
10.1080/10635150601156313. 17366135
-
Conditioned genome reconstruction: how to avoid choosing the conditioning genome. M Spencer D Bryant E Susko, Syst Biol 2007 56 1 25 43 10.1080/10635150601156313 17366135
-
(2007)
Syst Biol
, vol.56
, Issue.1
, pp. 25-43
-
-
Spencer, M.1
Bryant, D.2
Susko, E.3
-
6
-
-
0028361182
-
Recovering evolutionary trees under a more realistic model of sequence evolution
-
19391266
-
Recovering evolutionary trees under a more realistic model of sequence evolution. PJ Lockhart MA Steel MD Hendy D Penny, Mol Biol Evol 1994 11 4 605 612 19391266
-
(1994)
Mol Biol Evol
, vol.11
, Issue.4
, pp. 605-612
-
-
Lockhart, P.J.1
Steel, M.A.2
Hendy, M.D.3
Penny, D.4
-
7
-
-
1842505237
-
Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction
-
10.1093/molbev/msh061. 14739244
-
Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. JA Lake MC Rivera, Mol Biol Evol 2004 21 4 681 690 10.1093/molbev/msh061 14739244
-
(2004)
Mol Biol Evol
, vol.21
, Issue.4
, pp. 681-690
-
-
Lake, J.A.1
Rivera, M.C.2
-
8
-
-
13844306928
-
New methods ring changes for the tree of life
-
10.1016/j.tree.2005.01.007. 16701350
-
New methods ring changes for the tree of life. JO McInerney M Wilkinson, Trends Ecol Evol 2005 20 3 105 107 10.1016/j.tree.2005.01.007 16701350
-
(2005)
Trends Ecol Evol
, vol.20
, Issue.3
, pp. 105-107
-
-
McInerney, J.O.1
Wilkinson, M.2
-
9
-
-
34247180015
-
The origin of eukaryotes: A reappraisal
-
10.1038/nrg2071. 17429433
-
The origin of eukaryotes: a reappraisal. C de Duve, Nat Rev Genet 2007 8 5 395 403 10.1038/nrg2071 17429433
-
(2007)
Nat Rev Genet
, vol.8
, Issue.5
, pp. 395-403
-
-
De Duve, C.1
-
10
-
-
33646726959
-
Genomics and the irreducible nature of eukaryote cells
-
10.1126/science.1121674. 16709776
-
Genomics and the irreducible nature of eukaryote cells. CG Kurland LJ Collins D Penny, Science 2006 312 5776 1011 1014 10.1126/science.1121674 16709776
-
(2006)
Science
, vol.312
, Issue.5776
, pp. 1011-1014
-
-
Kurland, C.G.1
Collins, L.J.2
Penny, D.3
-
11
-
-
20344361920
-
Does the 'Ring of Life' ring true?
-
10.1016/j.tim.2005.03.012. 15936656
-
Does the 'Ring of Life' ring true? E Bapteste DA Walsh, Trends Microbiol 2005 13 6 256 261 10.1016/j.tim.2005.03.012 15936656
-
(2005)
Trends Microbiol
, vol.13
, Issue.6
, pp. 256-261
-
-
Bapteste, E.1
Walsh, D.A.2
-
12
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
10.1038/nrg1603. 15861208
-
Phylogenomics and the reconstruction of the tree of life. F Delsuc H Brinkmann H Philippe, Nat Rev Genet 2005 6 5 361 375 10.1038/nrg1603 15861208
-
(2005)
Nat Rev Genet
, vol.6
, Issue.5
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
13
-
-
4544313053
-
The ring of life provides evidence for a genome fusion origin of eukaryotes
-
10.1038/nature02848. 15356622
-
The ring of life provides evidence for a genome fusion origin of eukaryotes. MC Rivera JA Lake, Nature 2004 431 7005 152 155 10.1038/nature02848 15356622
-
(2004)
Nature
, vol.431
, Issue.7005
, pp. 152-155
-
-
Rivera, M.C.1
Lake, J.A.2
-
14
-
-
33644999199
-
On conditioned reconstruction, gene content data, and the recovery of fusion genomes
-
10.1016/j.ympev.2005.11.020. 16414287
-
On conditioned reconstruction, gene content data, and the recovery of fusion genomes. CD Bailey MG Fain P Houde, Mol Phylogenet Evol 2006 39 1 263 270 10.1016/j.ympev.2005.11.020 16414287
-
(2006)
Mol Phylogenet Evol
, vol.39
, Issue.1
, pp. 263-270
-
-
Bailey, C.D.1
Fain, M.G.2
Houde, P.3
-
15
-
-
57049148533
-
The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods
-
10.1186/1471-2148-8-312. 19014489
-
The tree of genomes: an empirical comparison of genome-phylogeny reconstruction methods. A McCann JA Cotton JO McInerney, BMC Evol Biol 2008 8 312 10.1186/1471-2148-8-312 19014489
-
(2008)
BMC Evol Biol
, vol.8
, pp. 312
-
-
McCann, A.1
Cotton, J.A.2
McInerney, J.O.3
-
16
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
10.1186/1471-2148-1-8. 11734060
-
Genome trees constructed using five different approaches suggest new major bacterial clades. YI Wolf IB Rogozin NV Grishin RL Tatusov EV Koonin, BMC Evol Biol 2001 1 8 10.1186/1471-2148-1-8 11734060
-
(2001)
BMC Evol Biol
, vol.1
, pp. 8
-
-
Wolf, Y.I.1
Rogozin, I.B.2
Grishin, N.V.3
Tatusov, R.L.4
Koonin, E.V.5
-
17
-
-
0035843908
-
Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis
-
10.1126/science.1058543. 11352062
-
Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. H Ochman NA Moran, Science 2001 292 5519 1096 1099 10.1126/science.1058543 11352062
-
(2001)
Science
, vol.292
, Issue.5519
, pp. 1096-1099
-
-
Ochman, H.1
Moran, N.A.2
-
18
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
10.1126/science.1123061. 16513982
-
Toward automatic reconstruction of a highly resolved tree of life. FD Ciccarelli T Doerks C von Mering CJ Creevey B Snel P Bork, Science 2006 311 5765 1283 1287 10.1126/science.1123061 16513982
-
(2006)
Science
, vol.311
, Issue.5765
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
Von Mering, C.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
19
-
-
19044362395
-
Gene family content-based phylogeny of prokaryotes: The effect of criteria for inferring homology
-
10.1080/10635150590923335. 16012097
-
Gene family content-based phylogeny of prokaryotes: the effect of criteria for inferring homology. AL Hughes V Ekollu R Friedman JR Rose, Syst Biol 2005 54 2 268 276 10.1080/10635150590923335 16012097
-
(2005)
Syst Biol
, vol.54
, Issue.2
, pp. 268-276
-
-
Hughes, A.L.1
Ekollu, V.2
Friedman, R.3
Rose, J.R.4
-
20
-
-
0035479142
-
Deletional bias and the evolution of bacterial genomes
-
10.1016/S0168-9525(01)02447-7. 11585665
-
Deletional bias and the evolution of bacterial genomes. A Mira H Ochman NA Moran, Trends Genet 2001 17 10 589 596 10.1016/S0168-9525(01)02447-7 11585665
-
(2001)
Trends Genet
, vol.17
, Issue.10
, pp. 589-596
-
-
Mira, A.1
Ochman, H.2
Moran, N.A.3
-
21
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
-
10.1038/nature02917. 15496922
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. B Kolaczkowski JW Thornton, Nature 2004 431 7011 980 984 10.1038/nature02917 15496922
-
(2004)
Nature
, vol.431
, Issue.7011
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
22
-
-
17744400517
-
Likelihood, parsimony, and heterogeneous evolution
-
10.1093/molbev/msi123. 15746012
-
Likelihood, parsimony, and heterogeneous evolution. M Spencer E Susko AJ Roger, Mol Biol Evol 2005 22 5 1161 1164 10.1093/molbev/msi123 15746012
-
(2005)
Mol Biol Evol
, vol.22
, Issue.5
, pp. 1161-1164
-
-
Spencer, M.1
Susko, E.2
Roger, A.J.3
-
23
-
-
67749145407
-
A phylogenetic mixture model for gene family loss in parasitic bacteria
-
19435739
-
A phylogenetic mixture model for gene family loss in parasitic bacteria. M Spencer A Sangaralingam, Mol Biol Evol 2009 19435739
-
(2009)
Mol Biol Evol
-
-
Spencer, M.1
Sangaralingam, A.2
-
24
-
-
0030660581
-
A genomic perspective on protein families
-
10.1126/science.278.5338.631. 9381173
-
A genomic perspective on protein families. RL Tatusov EV Koonin DJ Lipman, Science 1997 278 5338 631 637 10.1126/science.278.5338.631 9381173
-
(1997)
Science
, vol.278
, Issue.5338
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
25
-
-
0043163718
-
Protein families and TRIBES in genome sequence space
-
10.1093/nar/gkg495. 12888524
-
Protein families and TRIBES in genome sequence space. AJ Enright V Kunin CA Ouzounis, Nucleic Acids Res 2003 31 15 4632 4638 10.1093/nar/gkg495 12888524
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.15
, pp. 4632-4638
-
-
Enright, A.J.1
Kunin, V.2
Ouzounis, C.A.3
-
26
-
-
27544465780
-
CoGenT++: An extensive and extensible data environment for computational genomics
-
10.1093/bioinformatics/bti579. 16216832
-
CoGenT++: an extensive and extensible data environment for computational genomics. L Goldovsky P Janssen D Ahren B Audit I Cases N Darzentas AJ Enright N Lopez-Bigas JM Peregrin-Alvarez M Smith, et al. Bioinformatics 2005 21 19 3806 3810 10.1093/bioinformatics/bti579 16216832
-
(2005)
Bioinformatics
, vol.21
, Issue.19
, pp. 3806-3810
-
-
Goldovsky, L.1
Janssen, P.2
Ahren, D.3
Audit, B.4
Cases, I.5
Darzentas, N.6
Enright, A.J.7
Lopez-Bigas, N.8
Peregrin-Alvarez, J.M.9
Smith, M.10
-
27
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
10.1093/nar/30.7.1575. 11917018
-
An efficient algorithm for large-scale detection of protein families. AJ Enright S Van Dongen CA Ouzounis, Nucleic Acids research 2002 30 7 10.1093/nar/30.7.1575 11917018
-
(2002)
Nucleic Acids Research
, vol.30
, Issue.7
-
-
Enright, A.J.1
Van Dongen, S.2
Ouzounis, C.A.3
-
29
-
-
0030807655
-
BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
-
9254330
-
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. O Gascuel, Mol Biol Evol 1997 14 7 685 695 9254330
-
(1997)
Mol Biol Evol
, vol.14
, Issue.7
, pp. 685-695
-
-
Gascuel, O.1
-
30
-
-
0003437299
-
-
Deaprtment of Genome Sciences, University of Washington, Seattle
-
PHYLIP (Phylogeny Inference Package), version 3.6, distributed by the author. J Felsenstein, Deaprtment of Genome Sciences, University of Washington, Seattle 2005
-
(2005)
PHYLIP (Phylogeny Inference Package), Version 3.6, Distributed by the Author
-
-
Felsenstein, J.1
-
32
-
-
33846072878
-
The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data
-
35 DATABASE 10.1093/nar/gkl889. 17090583
-
The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data. JR Cole B Chai RJ Farris Q Wang AS Kulam-Syed-Mohideen DM McGarrell AM Bandela E Cardenas GM Garrity JM Tiedje, Nucleic Acids Res 2007 35 Database 169 172 10.1093/nar/gkl889 17090583
-
(2007)
Nucleic Acids Res
, pp. 169-172
-
-
Cole, J.R.1
Chai, B.2
Farris, R.J.3
Wang, Q.4
Kulam-Syed-Mohideen, A.S.5
McGarrell, D.M.6
Bandela, A.M.7
Cardenas, E.8
Garrity, G.M.9
Tiedje, J.M.10
-
33
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
10.1080/10635150390235520. 14530136
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. S Guindon O Gascuel, Syst Biol 2003 52 5 696 704 10.1080/10635150390235520 14530136
-
(2003)
Syst Biol
, vol.52
, Issue.5
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
34
-
-
0019424782
-
Comparison of phylogenetic trees
-
DOI 10.1016/0025-5564(81)90043-2
-
Comparison of phylogenetic trees. DR Robinson LR Foulds, Mathematical Biosciences 1981 53 131 147 10.1016/0025-5564(81)90043-2 (Pubitemid 11129084)
-
(1981)
Mathematical Biosciences
, vol.53
, Issue.1-2
, pp. 131-147
-
-
Robinson, D.F.1
Foulds, L.R.2
-
35
-
-
9744258014
-
Genome reduction in prokaryotic obligatory intracellular parasites of humans: A comparative analysis
-
10.1099/ijs.0.63090-0. 15545414
-
Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis. KR Sakharkar PK Dhar VT Chow, Int J Syst Evol Microbiol 2004 54 Pt 6 1937 1941 10.1099/ijs.0.63090-0 15545414
-
(2004)
Int J Syst Evol Microbiol
, vol.54
, Issue.PART 6
, pp. 1937-1941
-
-
Sakharkar, K.R.1
Dhar, P.K.2
Chow, V.T.3
-
36
-
-
3042840997
-
Computational inference of scenarios for alpha-proteobacterial genome evolution
-
10.1073/pnas.0400975101. 15210995
-
Computational inference of scenarios for alpha-proteobacterial genome evolution. B Boussau EO Karlberg AC Frank BA Legault SG Andersson, Proc Natl Acad Sci USA 2004 101 26 9722 9727 10.1073/pnas.0400975101 15210995
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.26
, pp. 9722-9727
-
-
Boussau, B.1
Karlberg, E.O.2
Frank, A.C.3
Legault, B.A.4
Andersson, S.G.5
-
37
-
-
0036078078
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
-
12045149
-
Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. IK Jordan IB Rogozin YI Wolf EV Koonin, Genome Res 2002 12 6 962 968 12045149
-
(2002)
Genome Res
, vol.12
, Issue.6
, pp. 962-968
-
-
Jordan, I.K.1
Rogozin, I.B.2
Wolf, Y.I.3
Koonin, E.V.4
-
38
-
-
0036898759
-
Prokaryotic evolution in light of gene transfer
-
12446813
-
Prokaryotic evolution in light of gene transfer. JP Gogarten WF Doolittle JG Lawrence, Mol Biol Evol 2002 19 12 2226 2238 12446813
-
(2002)
Mol Biol Evol
, vol.19
, Issue.12
, pp. 2226-2238
-
-
Gogarten, J.P.1
Doolittle, W.F.2
Lawrence, J.G.3
-
39
-
-
30344486571
-
On the desirability of models for inferring genome phylogenies
-
10.1016/j.tim.2005.10.006. 16271477
-
On the desirability of models for inferring genome phylogenies. JO McInerney, Trends Microbiol 2006 14 1 1 2 10.1016/j.tim.2005.10.006 16271477
-
(2006)
Trends Microbiol
, vol.14
, Issue.1
, pp. 1-2
-
-
McInerney, J.O.1
-
41
-
-
45249114886
-
Uncovering rate variation of lateral gene transfer during bacterial genome evolution
-
18492275
-
Uncovering rate variation of lateral gene transfer during bacterial genome evolution. W Hao BG Golding, BMC Genomics 2008 9 235 18492275
-
(2008)
BMC Genomics
, vol.9
, Issue.235
-
-
Hao, W.1
Golding, B.G.2
|