-
1
-
-
0033920569
-
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
-
J Adachi PJ Waddell W Martin M Hasegawa 2000 Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA J Mol Evol 50 348 358
-
(2000)
J Mol Evol
, vol.50
, pp. 348-358
-
-
Adachi, J.1
Waddell, P.J.2
Martin, W.3
Hasegawa, M.4
-
2
-
-
0031470387
-
Archaea and the prokaryote-to-eukaryote transition
-
JR Brown WF Doolittle 1997 Archaea and the prokaryote-to-eukaryote transition Microbiol Mol Biol Rev 61 456 502
-
(1997)
Microbiol Mol Biol Rev
, vol.61
, pp. 456-502
-
-
Brown, J.R.1
Doolittle, W.F.2
-
5
-
-
1242352070
-
Origin and Phylogeny of Chloroplasts revealed by a simple correlation analysis of complete genome
-
KH Chu J Qi ZG Yu VV Anh 2004 Origin and Phylogeny of Chloroplasts revealed by a simple correlation analysis of complete genome Mol Biol Evol 21 200 206
-
(2004)
Mol Biol Evol
, vol.21
, pp. 200-206
-
-
Chu, K.H.1
Qi, J.2
Yu, Z.G.3
Anh, V.V.4
-
6
-
-
0036225307
-
Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns
-
J De Las Rivas JJ Lozano AR Ortiz 2002 Comparative analysis of chloroplast genomes: Functional annotation, genome-based phylogeny, and deduced evolutionary patterns Genome Res 12 567 583
-
(2002)
Genome Res
, vol.12
, pp. 567-583
-
-
De Las Rivas, J.1
Lozano, J.J.2
Ortiz, A.R.3
-
7
-
-
0032568439
-
Microbial genomes opened up
-
RF Doolittle 1998 Microbial genomes opened up Nature 392 339 342
-
(1998)
Nature
, vol.392
, pp. 339-342
-
-
Doolittle, R.F.1
-
8
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
RF Doolittle 1999 Phylogenetic classification and the universal tree Science 284 2124 2128
-
(1999)
Science
, vol.284
, pp. 2124-2128
-
-
Doolittle, R.F.1
-
9
-
-
0036700153
-
A genomic schism in birds revealed by phylogenetic analysis of DNA strings
-
SV Edwards B Fertil A Giron P Deschavanne 2002 A genomic schism in birds revealed by phylogenetic analysis of DNA strings Syst Biol 51 599 613
-
(2002)
Syst Biol
, vol.51
, pp. 599-613
-
-
Edwards, S.V.1
Fertil, B.2
Giron, A.3
Deschavanne, P.4
-
10
-
-
0038518196
-
Phylogenomics: Intersection of evolution and genomics
-
JA Eisen CM Fraser 2003 Phylogenomics: intersection of evolution and genomics Science 300 1706 1707
-
(2003)
Science
, vol.300
, pp. 1706-1707
-
-
Eisen, J.A.1
Fraser, C.M.2
-
12
-
-
0014211361
-
Construction of phylogenetic trees
-
FitchWM E Margoliash 1967 Construction of phylogenetic trees Science 155 279 284
-
(1967)
Science
, vol.155
, pp. 279-284
-
-
Fitchwm1
Margoliash, E.2
-
13
-
-
0033231209
-
Whole genome-based phylogenetic analysis of free-living microorganisms
-
ST Fitz-Gibbon CH House 1999 Whole genome-based phylogenetic analysis of free-living microorganisms Nucleic Acids Res 27 4218 4222
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 4218-4222
-
-
Fitz-Gibbon, S.T.1
House, C.H.2
-
14
-
-
0027073347
-
The endosymbiont hypothesis revisited
-
MW Gray 1992 The endosymbiont hypothesis revisited Int. Rev Cytol 141 233 357
-
(1992)
Int. Rev Cytol
, vol.141
, pp. 233-357
-
-
Gray, M.W.1
-
15
-
-
0032762209
-
Evolution of organellar genomes
-
MW Gray 1999 Evolution of organellar genomes Curr Opin Genet Dev 9 678 687
-
(1999)
Curr Opin Genet Dev
, vol.9
, pp. 678-687
-
-
Gray, M.W.1
-
16
-
-
0031794743
-
Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes
-
RS Gupta 1998 Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes Microbiol Mol Biol Rev 62 1435 1491
-
(1998)
Microbiol Mol Biol Rev
, vol.62
, pp. 1435-1491
-
-
Gupta, R.S.1
-
17
-
-
0034628462
-
Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution
-
C Lemieux C Otis M Turmel 2000 Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution Nature 403 649 652
-
(2000)
Nature
, vol.403
, pp. 649-652
-
-
Lemieux, C.1
Otis, C.2
Turmel, M.3
-
18
-
-
0035102453
-
An information-based sequence distance and its application to whole mitochondrial genome phylogeny
-
M Li JH Badger X Chen S Kwong P Kearney H Zhang 2001 An information-based sequence distance and its application to whole mitochondrial genome phylogeny Bioinformatics 17 149 154
-
(2001)
Bioinformatics
, vol.17
, pp. 149-154
-
-
Li, M.1
Badger, J.H.2
Chen, X.3
Kwong, S.4
Kearney, P.5
Zhang, H.6
-
19
-
-
0033918311
-
Whole-genome trees based on the occurrence of folds and orthologs, implications for comparing genomes at different levels
-
J Lin M Gerstein 2000 Whole-genome trees based on the occurrence of folds and orthologs, implications for comparing genomes at different levels Genome Res 10 808 818
-
(2000)
Genome Res
, vol.10
, pp. 808-818
-
-
Lin, J.1
Gerstein, M.2
-
20
-
-
0002160837
-
Gene transfer from organelles to the nucleus: How much, what happens, and why?
-
W Martin RG Herrmann 1998 Gene transfer from organelles to the nucleus: How much, what happens, and why? Plant Physiol 118 9 17
-
(1998)
Plant Physiol
, vol.118
, pp. 9-17
-
-
Martin, W.1
Herrmann, R.G.2
-
22
-
-
0037126071
-
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus
-
W Martin T Rujan E Richly A Hansen S Cornelsen T Lins D Leister B Stoebe M Hasegawa D Penny 2002 Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus Proc Natl Acad Sci USA 99 12246 12251
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 12246-12251
-
-
Martin, W.1
Rujan, T.2
Richly, E.3
Hansen, A.4
Cornelsen, S.5
Lins, T.6
Leister, D.7
Stoebe, B.8
Hasegawa, M.9
Penny, D.10
-
23
-
-
0032544117
-
Two empires or the three
-
E Mayr 1998 Two empires or the three Proc Natl Acad Sci USA 95 9720 9723
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 9720-9723
-
-
Mayr, E.1
-
24
-
-
0035689472
-
Primary and secondary endosymbiosis and the origin of plastids
-
GI McFadden 2001a Primary and secondary endosymbiosis and the origin of plastids J Phycol 37 951 959
-
(2001)
J Phycol
, vol.37
, pp. 951-959
-
-
McFadden, G.I.1
-
25
-
-
0035140942
-
Chloroplast origin and integration
-
GI McFadden 2001b Chloroplast origin and integration Plant Physiol 125 50 53
-
(2001)
Plant Physiol
, vol.125
, pp. 50-53
-
-
McFadden, G.I.1
-
26
-
-
0034604170
-
The origin of red algae and the evolution of chloroplasts
-
DH Moreira H Le Guyader H Philippe 2000 The origin of red algae and the evolution of chloroplasts Nature 405 69 72
-
(2000)
Nature
, vol.405
, pp. 69-72
-
-
Moreira, D.H.1
Le Guyader, H.2
Philippe, H.3
-
28
-
-
0033591094
-
Is it the time to uproot the tree of life?
-
E Pennisi 1999 Is it the time to uproot the tree of life? Science 284 1305 1308
-
(1999)
Science
, vol.284
, pp. 1305-1308
-
-
Pennisi, E.1
-
29
-
-
3242890106
-
CVTree: A phylogenetic tree reconstruction tool based on whole genomes
-
J Qi H Luo B Hao 2004a CVTree: a phylogenetic tree reconstruction tool based on whole genomes Nucleic Acids Res 32 W45 W47
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Qi, J.1
Luo, H.2
Hao, B.3
-
30
-
-
1242335920
-
Whole proteome prokaryote phylogeny without sequence alignment: A K-string composition approach
-
J Qi B Wang B Hao 2004b Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach J Mol Evol 58 1 11
-
(2004)
J Mol Evol
, vol.58
, pp. 1-11
-
-
Qi, J.1
Wang, B.2
Hao, B.3
-
31
-
-
0035546223
-
Detection of lateral gene transfer among microbial genomes
-
MA Ragan 2001 Detection of lateral gene transfer among microbial genomes Curr Opin, Gen Dev 11 620 626
-
(2001)
Curr Opin, Gen Dev
, vol.11
, pp. 620-626
-
-
Ragan, M.A.1
-
32
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
N Saitou 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
-
35
-
-
0036166508
-
Integrated gene species phylogenies from unaligned whole genome protein sequences
-
GW Stuart K Moffet S Baker 2002a Integrated gene species phylogenies from unaligned whole genome protein sequences Bioinformatics 18 100 108
-
(2002)
Bioinformatics
, vol.18
, pp. 100-108
-
-
Stuart, G.W.1
Moffet, K.2
Baker, S.3
-
36
-
-
0036213976
-
A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes
-
GW Stuart K Moffet JJ Leader 2002b A comprehensive vertebrate phylogeny using vector representations of protein sequences from whole genomes Mol Biol Evol 19 554 562
-
(2002)
Mol Biol Evol
, vol.19
, pp. 554-562
-
-
Stuart, G.W.1
Moffet, K.2
Leader, J.J.3
-
37
-
-
0032778047
-
The genomic tree as revealed from whole proteome comparisons
-
F Tekaia A Lazcano B Dujon 1999 The genomic tree as revealed from whole proteome comparisons Genome Res 9 550 557
-
(1999)
Genome Res
, vol.9
, pp. 550-557
-
-
Tekaia, F.1
Lazcano, A.2
Dujon, B.3
-
38
-
-
0033621040
-
The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes
-
M Turmel C Otis C Lemieux 1999 The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes Proc Natl Acad Sci USA 96 10248 10253
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 10248-10253
-
-
Turmel, M.1
Otis, C.2
Lemieux, C.3
-
39
-
-
0037143760
-
The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants
-
M Turmel C Otis C Lemieux 2002 The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: Insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants Proc Natl Acad Sci USA 99 11275 11280
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 11275-11280
-
-
Turmel, M.1
Otis, C.2
Lemieux, C.3
-
41
-
-
0023184331
-
Bacterial evolution
-
CR Woese 1987 Bacterial evolution Microbiol Rev 51 221 271
-
(1987)
Microbiol Rev
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
42
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
-
CR Woese O Kandler ML Wheelis 1990 Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya Proc Natl Acad Sci USA 87 4576 4579
-
(1990)
Proc Natl Acad Sci USA
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
43
-
-
0035898770
-
Distance, correlation and mutual information among portraits of organisms based on complete genomes
-
ZG Yu P Jiang 2001 Distance, correlation and mutual information among portraits of organisms based on complete genomes Phys Lett A 286 34 46
-
(2001)
Phys Lett a
, vol.286
, pp. 34-46
-
-
Yu, Z.G.1
Jiang, P.2
-
44
-
-
42749106529
-
Multifractal and correlation analysis of protein sequences from complete genome
-
ZG Yu V Anh KS Lau 2003a Multifractal and correlation analysis of protein sequences from complete genome Phys Rev E 68 021913
-
(2003)
Phys Rev e
, vol.68
, pp. 021913
-
-
Yu, Z.G.1
Anh, V.2
Lau, K.S.3
-
45
-
-
0142091486
-
The genomic tree of living organisms based on a fractal model
-
ZG Yu V Anh KS Lau KH Chu 2003b The genomic tree of living organisms based on a fractal model Phys Lett A 317 293 302
-
(2003)
Phys Lett a
, vol.317
, pp. 293-302
-
-
Yu, Z.G.1
Anh, V.2
Lau, K.S.3
Chu, K.H.4
-
46
-
-
0345256581
-
Chaos game representation, and multifractal and correlation analysis of protein sequences from complete genome based on detailed HP model
-
ZG Yu V Anh KS Lau 2004 Chaos game representation, and multifractal and correlation analysis of protein sequences from complete genome based on detailed HP model J Theor Biol 226 341 348
-
(2004)
J Theor Biol
, vol.226
, pp. 341-348
-
-
Yu, Z.G.1
Anh, V.2
Lau, K.S.3
|