-
1
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese CR, Fox GE: Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A 1977, 74: 5088-5090
-
(1977)
Proc. Natl. Acad. Sci. U S A
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
2
-
-
0023184331
-
Bacterial evolution
-
Woese CR: Bacterial evolution. Microbiol Rev 1987, 51: 221-271
-
(1987)
Microbiol. Rev.
, vol.51
, pp. 221-271
-
-
Woese, C.R.1
-
4
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle WF: Phylogenetic classification and the universal tree. Science 1999, 284: 2124-2129
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
5
-
-
0031895203
-
Bacterial phylogeny based on comparative sequence analysis
-
Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH: Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 1998, 19: 554-568
-
(1998)
Electrophoresis
, vol.19
, pp. 554-568
-
-
Ludwig, W.1
Strunk, O.2
Klugbauer, S.3
Klugbauer, N.4
Weizenegger, M.5
Neumaier, J.6
Bachleitner, M.7
Schleifer, K.H.8
-
6
-
-
0031769997
-
Evolutionary anomalies among the aminoacyl-tRNA synthetases
-
Doolittle RF, Handy J: Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr Opin Genet Dev 1998, 8: 630-636
-
(1998)
Curr. Opin. Genet. Dev.
, vol.8
, pp. 630-636
-
-
Doolittle, R.F.1
Handy, J.2
-
7
-
-
0030868589
-
Comparison of archaeal and bacterial genomes: Computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea
-
Koonin EV, Mushegian AR, Galperin MY, Walker DR: Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea. Mol Microbiol 1997, 25: 619-637
-
(1997)
Mol. Microbiol.
, vol.25
, pp. 619-637
-
-
Koonin, E.V.1
Mushegian, A.R.2
Galperin, M.Y.3
Walker, D.R.4
-
8
-
-
0034542621
-
Horizontal transfer of archaeal genes into the deinococcaceae: Detection by molecular and computer-based approaches
-
Olendzenski L, Liu L, Zhaxybayeva O, Murphey R, Shin DG, Gogarten JP: Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches. J Mol Evol 2000, 51: 587-599
-
(2000)
J. Mol. Evol.
, vol.51
, pp. 587-599
-
-
Olendzenski, L.1
Liu, L.2
Zhaxybayeva, O.3
Murphey, R.4
Shin, D.G.5
Gogarten, J.P.6
-
9
-
-
0034703744
-
Evolutionary implications of the frequent horizontal transfer of mismatch repair genes
-
Denamur E, Lecointre G, Darlu P, Tenaillon O, Acquaviva C, Sayada C, Sunjevaric I, Rothstein R, Elion J, Taddei F, et al: Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell 2000, 103: 711-721
-
(2000)
Cell
, vol.103
, pp. 711-721
-
-
Denamur, E.1
Lecointre, G.2
Darlu, P.3
Tenaillon, O.4
Acquaviva, C.5
Sayada, C.6
Sunjevaric, I.7
Rothstein, R.8
Elion, J.9
Taddei, F.10
-
10
-
-
0035225012
-
Two C or not two C: Recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
-
research0033.1-research0033.14
-
Makarova KS, Ponomarev VA, Koonin EV: Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol 2001, 2: research0033.1-0033.14
-
(2001)
Genome Biol.
, vol.2
-
-
Makarova, K.S.1
Ponomarev, V.A.2
Koonin, E.V.3
-
11
-
-
0034565944
-
The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome
-
Brochier C, Philippe H, Moreira D: The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet 2000, 16: 529-533
-
(2000)
Trends Genet.
, vol.16
, pp. 529-533
-
-
Brochier, C.1
Philippe, H.2
Moreira, D.3
-
12
-
-
0032830481
-
Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
-
Wolf YI, Aravind L, Grishin NV, Koonin EV: Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res 1999, 9: 689-710
-
(1999)
Genome Res.
, vol.9
, pp. 689-710
-
-
Wolf, Y.I.1
Aravind, L.2
Grishin, N.V.3
Koonin, E.V.4
-
14
-
-
0032778047
-
The genomic tree as revealed from whole proteome comparisons
-
Tekaia F, Lazcano A, Dujon B: The genomic tree as revealed from whole proteome comparisons. Genome Res 1999, 9: 550-557
-
(1999)
Genome Res.
, vol.9
, pp. 550-557
-
-
Tekaia, F.1
Lazcano, A.2
Dujon, B.3
-
15
-
-
0032900532
-
Genome phylogeny based on gene content
-
[see comments]
-
Snel B, Bork P, Huynen MA: Genome phylogeny based on gene content [see comments]. Nat Genet 1999, 21: 108-110
-
(1999)
Nat. Genet.
, vol.21
, pp. 108-110
-
-
Snel, B.1
Bork, P.2
Huynen, M.A.3
-
16
-
-
0033231209
-
Whole genome-based phylogenetic analysis of free-living microorganisms
-
Fitz-Gibbon ST, House CH: Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 1999, 27: 4218-4222
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4218-4222
-
-
Fitz-Gibbon, S.T.1
House, C.H.2
-
17
-
-
0033918311
-
Whole-genome trees based on the occurrence of folds and orthologs: Implications for comparing genomes on different levels
-
Lin J, Gerstein M: Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 2000, 10: 808-818
-
(2000)
Genome Res.
, vol.10
, pp. 808-818
-
-
Lin, J.1
Gerstein, M.2
-
18
-
-
0034724342
-
An archaeal genomic signature
-
Graham DE, Overbeek R, Olsen GJ, Woese CR: An archaeal genomic signature. Proc Natl Acad Sci U S A 2000, 97: 3304-3308
-
(2000)
Proc. Natl. Acad. Sci. U S A
, vol.97
, pp. 3304-3308
-
-
Graham, D.E.1
Overbeek, R.2
Olsen, G.J.3
Woese, C.R.4
-
20
-
-
0025300402
-
Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
-
Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 1990, 87: 4576-4579
-
(1990)
Proc. Natl. Acad. Sci. U S A
, vol.87
, pp. 4576-4579
-
-
Woese, C.R.1
Kandler, O.2
Wheelis, M.L.3
-
21
-
-
0031678692
-
SplitsTree: Analyzing and visualizing evolutionary data
-
Huson DH: SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 1998, 14: 68-73
-
(1998)
Bioinformatics
, vol.14
, pp. 68-73
-
-
Huson, D.H.1
-
22
-
-
0031828312
-
The mosaic nature of the eukaryotic nucleus
-
Ribeiro S, Golding GB: The mosaic nature of the eukaryotic nucleus. Mol Biol Evol 1998, 15: 779-788
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 779-788
-
-
Ribeiro, S.1
Golding, G.B.2
-
24
-
-
0031002417
-
Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment
-
Strimmer K, von Haeseler A: Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A 1997, 94: 6815-6819
-
(1997)
Proc. Natl. Acad. Sci. U S A
, vol.94
, pp. 6815-6819
-
-
Strimmer, K.1
von Haeseler, A.2
-
25
-
-
0030623948
-
SEALS: A system for easy analysis of lots of sequences
-
Walker DR, Koonin EV: SEALS: a system for easy analysis of lots of sequences. ISMB 1997, 5: 333-339
-
(1997)
ISMB
, vol.5
, pp. 333-339
-
-
Walker, D.R.1
Koonin, E.V.2
-
26
-
-
0030660581
-
A genomic perspective on protein families
-
Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997, 278: 631-637
-
(1997)
Science
, vol.278
, pp. 631-637
-
-
Tatusov, R.L.1
Koonin, E.V.2
Lipman, D.J.3
-
27
-
-
0033956060
-
The COG database: A tool for genome-scale analysis of protein functions and evolution
-
Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28: 33-36
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 33-36
-
-
Tatusov, R.L.1
Galperin, M.Y.2
Natale, D.A.3
Koonin, E.V.4
-
28
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29: 22-28
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
30
-
-
0029933671
-
Effective protein sequence comparison
-
Pearson WR: Effective protein sequence comparison. Methods Enzymol 1996, 266: 227-258
-
(1996)
Methods Enzymol.
, vol.266
, pp. 227-258
-
-
Pearson, W.R.1
-
31
-
-
0034849408
-
MrBayes: Bayesian inference of phylogenetic trees
-
Huelsenbeck JP, Ronquist F: MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17: 754-755
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
32
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985, 39: 783-791
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
33
-
-
0035861441
-
Resolution of the early placental mammal radiation using Bayesian phylogenetics
-
Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, et al: Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 2001, 294: 2348-2351
-
(2001)
Science
, vol.294
, pp. 2348-2351
-
-
Murphy, W.J.1
Eizirik, E.2
O'Brien, S.J.3
Madsen, O.4
Scally, M.5
Douady, C.J.6
Teeling, E.7
Ryder, O.A.8
Stanhope, M.J.9
de Jong, W.W.10
-
34
-
-
0029818407
-
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
-
Rannala B, Yang Z: Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J Mol Evol 1996, 43:304-311
-
(1996)
J. Mol. Evol.
, vol.43
, pp. 304-311
-
-
Rannala, B.1
Yang, Z.2
-
35
-
-
0035861514
-
The closest living relatives of land plants
-
Karol KG, McCourt RM, Cimino MT, Delwiche CF: The closest living relatives of land plants. Science 2001, 294: 351-2353
-
(2001)
Science
, vol.294
, pp. 2351-2353
-
-
Karol, K.G.1
McCourt, R.M.2
Cimino, M.T.3
Delwiche, C.F.4
-
36
-
-
0033598755
-
Recurrent invasion and extinction of a selfish gene
-
Goddard MR, Burt A: Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci U S A 1999, 96: 13880-13885
-
(1999)
Proc. Natl. Acad. Sci. U S A
, vol.96
, pp. 13880-13885
-
-
Goddard, M.R.1
Burt, A.2
-
37
-
-
0032540298
-
Witnessing the evolution of transcription in mitochondria: The mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. Encodes a T7-like RNA polymerase
-
Rousvoal S, Oudot M, Fontaine J, Kloareg B, Goer SL: Witnessing the evolution of transcription in mitochondria: the mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. Encodes a T7-like RNA polymerase. J Mol Biol 1998, 277: 1047-1057
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 1047-1057
-
-
Rousvoal, S.1
Oudot, M.2
Fontaine, J.3
Kloareg, B.4
Goer, S.L.5
-
38
-
-
0031464189
-
On the evolution of the single-subunit RNA polymerases
-
Cermakian N, Ikeda TM, Miramontes P, Lang BF, Gray MW, Cedergren R: On the evolution of the single-subunit RNA polymerases. J Mol Evol 1997, 45: 671-681
-
(1997)
J. Mol. Evol.
, vol.45
, pp. 671-681
-
-
Cermakian, N.1
Ikeda, T.M.2
Miramontes, P.3
Lang, B.F.4
Gray, M.W.5
Cedergren, R.6
-
39
-
-
0024601035
-
Mitochondrial RNA polymerase: Dual role in transcription and replication
-
Schinkel AH, Tabak HF: Mitochondrial RNA polymerase: dual role in transcription and replication. Trends Genet 1989, 5: 149-154
-
(1989)
Trends Genet.
, vol.5
, pp. 149-154
-
-
Schinkel, A.H.1
Tabak, H.F.2
-
40
-
-
0031865507
-
Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria
-
Gupta RS, Johari V: Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria. J Mol Evol 1998, 46: 716-720
-
(1998)
J. Mol. Evol.
, vol.46
, pp. 716-720
-
-
Gupta, R.S.1
Johari, V.2
-
41
-
-
0033030130
-
Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): Implications regarding the origin of photosynthesis
-
Gupta RS, Mukhtar T, Singh B: Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis. Mol Microbiol 1999, 32: 893-906
-
(1999)
Mol. Microbiol.
, vol.32
, pp. 893-906
-
-
Gupta, R.S.1
Mukhtar, T.2
Singh, B.3
-
42
-
-
0033935581
-
The natural evolutionary relationships among prokaryotes
-
Gupta RS: The natural evolutionary relationships among prokaryotes. Crit Rev Microbiol 2000, 26: 111-131
-
(2000)
Crit. Rev. Microbiol.
, vol.26
, pp. 111-131
-
-
Gupta, R.S.1
-
43
-
-
0034622999
-
Molecular evidence for the early evolution of photosynthesis
-
Xiong J, Fischer WM, Inoue K, Nakahara M, Bauer CE: Molecular evidence for the early evolution of photosynthesis. Science 2000, 289: 1724-1730
-
(2000)
Science
, vol.289
, pp. 1724-1730
-
-
Xiong, J.1
Fischer, W.M.2
Inoue, K.3
Nakahara, M.4
Bauer, C.E.5
-
45
-
-
0036137155
-
Eubacterial phylogeny based on translational apparatus proteins
-
Brochier C, Bapteste E, Moreira D, Philippe H: Eubacterial phylogeny based on translational apparatus proteins. Trends Genet 2002, 18: 1-5
-
(2002)
Trends Genet.
, vol.18
, pp. 1-5
-
-
Brochier, C.1
Bapteste, E.2
Moreira, D.3
Philippe, H.4
-
46
-
-
0348044549
-
Genome trees constructed using five different approaches suggest new major bacterial clades
-
Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV: Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 2001, 1: 8
-
(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
-
47
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: Quantification and classification
-
Koonin EV, Makarova KS, Aravind L: Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 2001, 55: 709-742
-
(2001)
Annu. Rev. Microbiol.
, vol.55
, pp. 709-742
-
-
Koonin, E.V.1
Makarova, K.S.2
Aravind, L.3
-
48
-
-
84959798530
-
Cases in which parsimony and compatibility methods will be positively misleading
-
Felsenstein J: Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 1978, 27: 401-410
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
49
-
-
0031793259
-
Cloning and sequencing of the homologues of both the bacterial and eukaryotic initiation factor genes (hIF-2 and heIF-2 gamma) from archaeal Halobacterium halobium
-
Hasegawa Y, Sawaoka N, Kado N, Ochi M, Itoh T: Cloning and sequencing of the homologues of both the bacterial and eukaryotic initiation factor genes (hIF-2 and heIF-2 gamma) from archaeal Halobacterium halobium. Biochem Mol Biol Int 1998, 46: 495-507
-
(1998)
Biochem. Mol. Biol. Int.
, vol.46
, pp. 495-507
-
-
Hasegawa, Y.1
Sawaoka, N.2
Kado, N.3
Ochi, M.4
Itoh, T.5
-
50
-
-
0029847554
-
Selfish operons: Horizontal transfer may drive the evolution of gene clusters
-
Lawrence JG, Roth JR: Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 1996, 143: 1843-1860
-
(1996)
Genetics
, vol.143
, pp. 1843-1860
-
-
Lawrence, J.G.1
Roth, J.R.2
-
51
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 3389-3402
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
52
-
-
0025183708
-
Basic local alignment search tool
-
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215: 403-410
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
53
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
54
-
-
0034894278
-
PAL: An object-oriented programming library for molecular evolution and phylogenetics
-
Drummond A, Strimmer K: PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 2001, 17: 662-663
-
(2001)
Bioinformatics
, vol.17
, pp. 662-663
-
-
Drummond, A.1
Strimmer, K.2
-
55
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. CABIOS 1992, 8: 275-282
-
(1992)
CABIOS
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
56
-
-
0029836454
-
Quartet puzzling: Quartet A maximum-likelihood method for reconstructing tree topologies
-
Strimmer K, von Haeseler A: Quartet puzzling: quartet A maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 1996, 964-969
-
(1996)
Molecular Biology and Evolution
, pp. 964-969
-
-
Strimmer, K.1
von Haeseler, A.2
-
57
-
-
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 1994, 39: 306-314
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.1
|