-
1
-
-
0034897709
-
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
-
M. Anisimova, J.P. Bielawski, and Z. Yang Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution Mol. Biol. Evol. 18 2001 1585 1592
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1585-1592
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
2
-
-
0036272936
-
Accuracy and power of Bayes prediction of amino acid sites under positive selection
-
M. Anisimova, J.P. Bielawski, and Z. Yang Accuracy and power of Bayes prediction of amino acid sites under positive selection Mol. Biol. Evol. 19 2002 950 958
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 950-958
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
3
-
-
0042208362
-
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
-
M. Anisimova, R. Nielsen, and Z. Yang Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites Genetics 164 2003 1229 1236
-
(2003)
Genetics
, vol.164
, pp. 1229-1236
-
-
Anisimova, M.1
Nielsen, R.2
Yang, Z.3
-
4
-
-
0033533517
-
Neutral evolution of model proteins: Diffusion in sequence space and overdispersion
-
U. Bastolla, M. Vendruscolo, and H.E. Roman Neutral evolution of model proteins: diffusion in sequence space and overdispersion J. Theor. Biol. 200 1999 49 64
-
(1999)
J. Theor. Biol.
, vol.200
, pp. 49-64
-
-
Bastolla, U.1
Vendruscolo, M.2
Roman, H.E.3
-
5
-
-
0025939530
-
Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae
-
A.G. Clark, and T.-H. Kao Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae Proc. Natl. Acad. Sci. U. S. A. 88 1991 9823 9827
-
(1991)
Proc. Natl. Acad. Sci. U. S. A.
, vol.88
, pp. 9823-9827
-
-
Clark, A.G.1
Kao, T.-H.2
-
6
-
-
84959747425
-
Toward defining the course of evolution: Minimum change for a specific tree topology
-
W.M. Fitch Toward defining the course of evolution: minimum change for a specific tree topology Syst. Zool. 20 1971 406 416
-
(1971)
Syst. Zool.
, vol.20
, pp. 406-416
-
-
Fitch, W.M.1
-
7
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
N. Goldman, and Z. Yang A codon-based model of nucleotide substitution for protein-coding DNA sequences Mol. Biol. Evol. 11 1994 725 736
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
8
-
-
0002329356
-
Minimum mutation fits to a given tree
-
J.A. Hartigan Minimum mutation fits to a given tree Biometrics 29 1973 53 65
-
(1973)
Biometrics
, vol.29
, pp. 53-65
-
-
Hartigan, J.A.1
-
9
-
-
0023764283
-
Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
-
A.L. Hughes, and M. Nei Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection Nature 335 1988 167 170
-
(1988)
Nature
, vol.335
, pp. 167-170
-
-
Hughes, A.L.1
Nei, M.2
-
10
-
-
0040771786
-
Nucleotide substitution at major histocompatibility complex class II loci: Evidence for overdominant selection
-
A.L. Hughes, and M. Nei Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection Proc. Natl. Acad. Sci. U. S. A. 86 1989 958 962
-
(1989)
Proc. Natl. Acad. Sci. U. S. A.
, vol.86
, pp. 958-962
-
-
Hughes, A.L.1
Nei, M.2
-
11
-
-
17744396121
-
Not so different after all: A comparison of methods for detecting amino acid sites under selection
-
S.L. Kosakovsky Pond, and S.D.W. Frost Not so different after all: a comparison of methods for detecting amino acid sites under selection Mol. Biol. Evol. 22 2005 1208 1222
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1208-1222
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
-
12
-
-
17444412589
-
Detecting amino acid sites under positive selection and purifying selection
-
T. Massingham, and N. Goldman Detecting amino acid sites under positive selection and purifying selection Genetics 169 2005 1753 1762
-
(2005)
Genetics
, vol.169
, pp. 1753-1762
-
-
Massingham, T.1
Goldman, N.2
-
13
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
S.V. Muse, and S.B. Gaut A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome Mol. Biol. Evol. 11 1994 715 724
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 715-724
-
-
Muse, S.V.1
Gaut, S.B.2
-
14
-
-
14544272929
-
Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
-
M. Porto, H.E. Roman, M. Vendruscolo, and U. Bastolla Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences Mol. Biol. Evol. 22 2004 630 638
-
(2004)
Mol. Biol. Evol.
, vol.22
, pp. 630-638
-
-
Porto, M.1
Roman, H.E.2
Vendruscolo, M.3
Bastolla, U.4
-
15
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
-
(1987)
Mol. Biol. Evol.
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
16
-
-
3042725369
-
New methods for detecting positive selection at single amino acid sites
-
Y. Suzuki New methods for detecting positive selection at single amino acid sites J. Mol. Evol. 59 2004 11 19
-
(2004)
J. Mol. Evol.
, vol.59
, pp. 11-19
-
-
Suzuki, Y.1
-
17
-
-
8444220853
-
Three-dimensional window analysis for detecting positive selection at structural regions of proteins
-
Y. Suzuki Three-dimensional window analysis for detecting positive selection at structural regions of proteins Mol. Biol. Evol. 21 2004 2352 2359
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 2352-2359
-
-
Suzuki, Y.1
-
18
-
-
0032849322
-
A method for detecting positive selection at single amino acid sites
-
Y. Suzuki, and T. Gojobori A method for detecting positive selection at single amino acid sites Mol. Biol. Evol. 16 1999 1315 1328
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1315-1328
-
-
Suzuki, Y.1
Gojobori, T.2
-
19
-
-
0035215112
-
Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acis sites
-
Y. Suzuki, and M. Nei Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acis sites Mol. Biol. Evol. 18 2001 2179 2185
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 2179-2185
-
-
Suzuki, Y.1
Nei, M.2
-
20
-
-
0036855372
-
Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
-
Y. Suzuki, and M. Nei Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites Mol. Biol. Evol. 19 2002 1865 1869
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1865-1869
-
-
Suzuki, Y.1
Nei, M.2
-
21
-
-
1942533483
-
False-positive selection identified by ML-based methods: Examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus
-
Y. Suzuki, and M. Nei False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus Mol. Biol. Evol. 21 2004 914 921
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 914-921
-
-
Suzuki, Y.1
Nei, M.2
-
22
-
-
0034904729
-
ADAPTSITE: Detecting natural selection at single amino acid sites
-
Y. Suzuki, T. Gojobori, and M. Nei ADAPTSITE: detecting natural selection at single amino acid sites Bioinformatics 17 2001 660 661
-
(2001)
Bioinformatics
, vol.17
, pp. 660-661
-
-
Suzuki, Y.1
Gojobori, T.2
Nei, M.3
-
23
-
-
0037230001
-
Pervasive adaptive evolution in mammalian fertilization proteins
-
W.J. Swanson, R. Nielsen, and Q. Yang Pervasive adaptive evolution in mammalian fertilization proteins Mol. Biol. Evol. 20 2003 18 20
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 18-20
-
-
Swanson, W.J.1
Nielsen, R.2
Yang, Q.3
-
24
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res. 22 1994 4673 4680
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
25
-
-
8544225780
-
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
-
W.S.W. Wong, Z. Yang, N. Goldman, and R. Nielsen Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites Genetics 168 2004 1041 1051
-
(2004)
Genetics
, vol.168
, pp. 1041-1051
-
-
Wong, W.S.W.1
Yang, Z.2
Goldman, N.3
Nielsen, R.4
-
26
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood Comput. Appl. Biosci. 13 1997 555 556
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
27
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Z. Yang, R. Nielsen, N. Goldman, and A.M. Pedersen Codon-substitution models for heterogeneous selection pressure at amino acid sites Genetics 155 2000 431 449
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.4
-
28
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
Z. Yang, W.S.W. Wong, and R. Nielsen Bayes empirical Bayes inference of amino acid sites under positive selection Mol. Biol. Evol. 22 2005 1107 1118
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.S.W.2
Nielsen, R.3
-
29
-
-
3042637218
-
Frequent false detection of positive selection by the likelihood method with branch-site models
-
J. Zhang Frequent false detection of positive selection by the likelihood method with branch-site models Mol. Biol. Evol. 21 2004 1332 1339
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1332-1339
-
-
Zhang, J.1
|