-
1
-
-
0031828312
-
The mosaic nature of the eukaryotic nucleus
-
Ribeiro S and 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
-
2
-
-
2242447089
-
Whole-genome analysis of photosynthetic prokaryotes
-
Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY and Blankenship RE: Whole-genome analysis of photosynthetic prokaryotes. Science 2002, 298:1616-1620.
-
(2002)
Science
, vol.298
, pp. 1616-1620
-
-
Raymond, J.1
Zhaxybayeva, O.2
Gogarten, J.P.3
Gerdes, S.Y.4
Blankenship, R.E.5
-
4
-
-
9144225618
-
Bootstrap, Bayesian probability and maximum likelihood mapping: Exploring new tools for comparative genome analyses
-
Zhaxybayeva O and Gogarten JP: Bootstrap, Bayesian probability and maximum likelihood mapping: Exploring new tools for comparative genome analyses. BMC Genomics 2002, 3:4.
-
(2002)
BMC Genomics
, vol.3
, pp. 4
-
-
Zhaxybayeva, O.1
Gogarten, J.P.2
-
5
-
-
0034831587
-
Defining the core of nontransferable prokaryotic genes: The euryarchaeal core
-
Nesbo CL, Boucher Y and Doolittle WF: Defining the core of nontransferable prokaryotic genes: the euryarchaeal core. J Mol Evol 2001, 53:340-350.
-
(2001)
J. Mol. Evol.
, vol.53
, pp. 340-350
-
-
Nesbo, C.L.1
Boucher, Y.2
Doolittle, W.F.3
-
6
-
-
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: 01-410.
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
7
-
-
0000074814
-
Likelihood and Inconsistency
-
Farris JS: Likelihood and Inconsistency. Cladistics 1999, 15:199-204.
-
(1999)
Cladistics
, vol.15
, pp. 199-204
-
-
Farris, J.S.1
-
8
-
-
0000215283
-
Success of Parsimony in the Four-Taxon Case: Long-Branch Repulsion by Likelihood in the Farris Zone
-
Siddall ME: Success of Parsimony in the Four-Taxon Case: Long-Branch Repulsion by Likelihood in the Farris Zone. Cladistics 1998, 14:209-220.
-
(1998)
Cladistics
, vol.14
, pp. 209-220
-
-
Siddall, M.E.1
-
9
-
-
0024152983
-
Phylogenies from molecular sequences: Inference and reliability
-
Felsenstein J: Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 1988, 22: 21-565.
-
(1988)
Annu. Rev. Genet.
, vol.22
, pp. 521-565
-
-
Felsenstein, J.1
-
10
-
-
0029113744
-
The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
-
Huelsenbeck JP: The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol Biol Evol 1995, 12: 43-849.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 843-849
-
-
Huelsenbeck, J.P.1
-
11
-
-
12044255023
-
Success of Phylogenetic Methods in the Four-Taxon Case
-
Huelsenbeck JP and Hillis DM: Success of Phylogenetic Methods in the Four-Taxon Case. Systematic Biology 1993, 42: 47-264.
-
(1993)
Systematic Biology
, vol.42
, pp. 247-264
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
12
-
-
0000909802
-
The pitfalls of molecular phylogeny based on four species as illustrated by the Cetacea/Artiodactyla relationships
-
Philippe H and Douzery E: The pitfalls of molecular phylogeny based on four species as illustrated by the Cetacea/Artiodactyla relationships. Journal of Mammalian Evolution 1994, 2:133-152.
-
(1994)
Journal of Mammalian Evolution
, vol.2
, pp. 133-152
-
-
Philippe, H.1
Douzery, E.2
-
13
-
-
0030207565
-
Instability of quartet analyses of molecular sequence data by the maximum likelihood method: The Cetacea/Artiodactyla relationships
-
Adachi J and Hasegawa M: Instability of quartet analyses of molecular sequence data by the maximum likelihood method: the Cetacea/Artiodactyla relationships. Mol Phylogenet Evol 1996, 6:72-76.
-
(1996)
Mol. Phylogenet. Evol.
, vol.6
, pp. 72-76
-
-
Adachi, J.1
Hasegawa, M.2
-
14
-
-
0032025857
-
Is it better to add taxa or characters to a difficult phylogenetic problem?
-
Graybeal A: Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 1998, 47:9-17.
-
(1998)
Syst. Biol.
, vol.47
, pp. 9-17
-
-
Graybeal, A.1
-
16
-
-
0037291976
-
Taxon sampling, bioinformatics, and phylogenomics
-
Rosenberg MS and Kumar S: Taxon sampling, bioinformatics, and phylogenomics. Syst Biol 2003, 52:119-124.
-
(2003)
Syst. Biol.
, vol.52
, pp. 119-124
-
-
Rosenberg, M.S.1
Kumar, S.2
-
17
-
-
0031002417
-
Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment
-
Strimmer K and 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
-
18
-
-
0002573156
-
Eric Weisstein's World of Mathematics
-
Eric Weisstein's World of Mathematics [http://mathworld.wolfram.com/]
-
-
-
-
20
-
-
0027241482
-
Monophyletic origins of the metazoa: An evolutionary link with fungi
-
Wainright PO, Hinkle G, Sogin ML and Stickel SK: Monophyletic origins of the metazoa: an evolutionary link with fungi. Science 1993, 260:340-342.
-
(1993)
Science
, vol.260
, pp. 340-342
-
-
Wainright, P.O.1
Hinkle, G.2
Sogin, M.L.3
Stickel, S.K.4
-
22
-
-
0034780910
-
Horizontal gene transfer in prokaryotes: Quantification and classification
-
Koonin EV, Makarova KS and 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
-
23
-
-
12944270421
-
Genome sequence of Halobacterium species NRC-1
-
Ng WV, Kennedy SP, Mahairas GG, Berquist B, Pan M, Shukla HD, Lasky SR, Baliga NS, Thorsson V, Sbrogna J, Swartzell S, Weir D, Hall J, Dahl TA, Welti R, Goo YA, Leithauser B, Keller K, Cruz R, Danson MJ, Hough DW, Maddocks DG, Jablonski PE, Krebs MP, Angevine CM, Dale H, Isenbarger TA, Peck RF, Pohlschroder M, Spudich JL, Jung KW, Alam M, Freitas T, Hou S, Daniels CJ, Dennis PP, Omer AD, Ebhardt H, Lowe TM, Liang P, Riley M, Hood L and DasSarma S: Genome sequence of Halobacterium species NRC-1. Proc Natl Acad Sci U S A 2000, 97:12176-12181.
-
(2000)
Proc. Natl. Acad. Sci. U S A
, vol.97
, pp. 12176-12181
-
-
Ng, W.V.1
Kennedy, S.P.2
Mahairas, G.G.3
Berquist, B.4
Pan, M.5
Shukla, H.D.6
Lasky, S.R.7
Baliga, N.S.8
Thorsson, V.9
Sbrogna, J.10
Swartzell, S.11
Weir, D.12
Hall, J.13
Dahl, T.A.14
Welti, R.15
Goo, Y.A.16
Leithauser, B.17
Keller, K.18
Cruz, R.19
Danson, M.J.20
Hough, D.W.21
Maddocks, D.G.22
Jablonski, P.E.23
Krebs, M.P.24
Angevine, C.M.25
Dale, H.26
Isenbarger, T.A.27
Peck, R.F.28
Pohlschroder, M.29
Spudich, J.L.30
Jung, K.W.31
Alam, M.32
Freitas, T.33
Hou, S.34
Daniels, C.J.35
Dennis, P.P.36
Omer, A.D.37
Ebhardt, H.38
Lowe, T.M.39
Liang, P.40
Riley, M.41
Hood, L.42
DasSarma, S.43
more..
-
24
-
-
0034178257
-
Homology a personal view on some of the problems
-
Fitch WM: Homology a personal view on some of the problems. Trends Genet 2000, 16:227-231.
-
(2000)
Trends Genet.
, vol.16
, pp. 227-231
-
-
Fitch, W.M.1
-
25
-
-
0037329108
-
Comparison of bayesian and maximum likelihood bootstrap measures of phylogenetic reliability
-
Douady CJ, Delsuc F, Boucher Y, Doolittle WF and Douzery EJ: Comparison of bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol Biol Evol 2003, 20:248-254.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 248-254
-
-
Douady, C.J.1
Delsuc, F.2
Boucher, Y.3
Doolittle, W.F.4
Douzery, E.J.5
-
26
-
-
0037329391
-
Bayes or bootstrap? A simulation study comparing the performance of bayesian markov chain monte carlo sampling and bootstrapping in assessing phylogenetic confidence
-
Alfaro ME, Zoller S and Lutzoni F: Bayes or bootstrap? A simulation study comparing the performance of bayesian markov chain monte carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 2003, 20:255-266.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 255-266
-
-
Alfaro, M.E.1
Zoller, S.2
Lutzoni, F.3
-
27
-
-
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 and Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25: 389-3402.
-
(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
-
28
-
-
9144266404
-
-
National Center for Biotechnology Information
-
National Center for Biotechnology Information [http://www.ncbi.nlm.nih.gov/]
-
-
-
-
29
-
-
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 and 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
-
30
-
-
0003437299
-
PHYLIP (Phylogeny Inference Package) version 3.6
-
Distributed by the author. Department of Genetics, University of Washington, Seattle
-
Felsenstein J: PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genetics, University of Washington, Seattle 1993.
-
(1993)
-
-
Felsenstein, J.1
-
31
-
-
0036205377
-
TREEPUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M and von Haeseler A: TREEPUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
von Haeseler, A.4
-
32
-
-
0034894278
-
PAL: An object-oriented programming library for molecular evolution and phylogenetics
-
Drummond A and 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
-
33
-
-
9144236968
-
-
GNUPLOT Central
-
GNUPLOT Central [http://www.gnuplot.info]
-
-
-
-
34
-
-
0030623948
-
SEALS: A system for easy analysis of lots of sequences
-
Walker DR and 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
-
35
-
-
1842720344
-
Integrated Genomics
-
Integrated Genomics [http://www.integratedgenomics.com/]
-
-
-
-
36
-
-
9144264299
-
-
The Institute for Genomic Research
-
The Institute for Genomic Research [http://www.tigr.org]
-
-
-
-
37
-
-
9144264942
-
-
DOE Joint Genome Institute
-
DOE Joint Genome Institute [http://www.jgi.doe.govJGI_microbial/html/index.html]
-
-
-
-
38
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck JP and 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
|