-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
Abascal, F., R. Zardoya, and D. Posada. 2005. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
0029974748
-
Model of amino acid substitution in proteins encoded by mitochondrial DNA
-
Adachi, J., and M. Hasegawa. 1996. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol. 42:459-468.
-
(1996)
J. Mol. Evol
, vol.42
, pp. 459-468
-
-
Adachi, J.1
Hasegawa, M.2
-
3
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike, H. 1974. A new look at the statistical model identification. IEEE Trans. Autom. Contr. 19:716-723.
-
(1974)
IEEE Trans. Autom. Contr
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
4
-
-
4444220955
-
Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
-
Anderson, F. E., and D. L. Swofford. 2004. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol. Phylogenet. Evol. 33:440-451.
-
(2004)
Mol. Phylogenet. Evol
, vol.33
, pp. 440-451
-
-
Anderson, F.E.1
Swofford, D.L.2
-
6
-
-
0036623259
-
Model misspecification and probabilistic tests of topology: Evidence from empirical data sets
-
Buckley T. R. 2002. Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Syst. Biol. 51:509-523.
-
(2002)
Syst. Biol
, vol.51
, pp. 509-523
-
-
Buckley, T.R.1
-
7
-
-
0028172520
-
Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene
-
Cao, Y., J. Adachi, A. Janke, S. Paabo, and M. Hasegawa. 1994. Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene. J. Mol. Evol. 39:519-527.
-
(1994)
J. Mol. Evol
, vol.39
, pp. 519-527
-
-
Cao, Y.1
Adachi, J.2
Janke, A.3
Paabo, S.4
Hasegawa, M.5
-
8
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna, R., H. Sugawara, T. Koike, R. Lopez, T. J. Gibson, D. G. Higgins, and J. D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
9
-
-
0000228203
-
A model of evolutionary change in proteins
-
M. O. Dayhoff, ed, National Biomedical Research Foundation, Washington, DC
-
Dayhoff, M. O., R. M. Schwartz, and B. C. Orcutt. 1978. A model of evolutionary change in proteins. Pages 345-352 in Atlas of protein sequence and structure (M. O. Dayhoff, ed.). National Biomedical Research Foundation, Washington, DC.
-
(1978)
Atlas of protein sequence and structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
10
-
-
33846818777
-
A combined empirical and mechanistic codon model
-
Doron-Faigenboim, A., and T. Pupko. 2007. A combined empirical and mechanistic codon model. Mol. Biol. Evol. 24:388-397.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 388-397
-
-
Doron-Faigenboim, A.1
Pupko, T.2
-
11
-
-
3042720475
-
-
Dujon, B, D. Sherman, G. Fischer, P. Durrens, S. Casaregola, I. Lafontaine, J. de Montigny, C. Marck, C. Neuvéglise, E. Talla, N. Goffard, L. Frangeul, M. Aigle, V. Anthouard, A. Babour, V. Barbe, S. Barnay, S. Blanchin, J.-M. Beckerich, E. Beyne, C. Bleykasten, A. Boisramé, J. Boyer, L. Cattolico, F. Confanioleri, A. de Daruvar, L. Despons, E. Fabre, C. Fairhead, H. Ferry-Dumazet, A. Groppi, F. Hantraye, C. Hennequin, N. Jauniaux, P. Joyet, R. Kachouri, A. Kerrest, R. Koszul, M. Lemaire, I. Lesur, L. Ma, H. Muller, J.-M. Nicaud, M. Nikolski, S. Oztas, O. Ozier-Kalogeropoulos, S. Pellenz, S. Potier, G.-F. Richard, M.-L. Straub, A. Suleau, D. Swennen, F. Tekaia, M. Wésolowski-Louvel, E. Westhof, B. Wirth, M. Zeniou-Meyer, I. Zivanovic, M. Bolotin-Fukuhara, A. Thierry, C. Bouchier, B. Caudron, C. Scarpelli, C. Gaillardin, J. Weissenbach, P. Wincker and J.-L. Souciet. Genome evolution in yeasts. Nature 430:35-44
-
Dujon, B., D. Sherman, G. Fischer, P. Durrens, S. Casaregola, I. Lafontaine, J. de Montigny, C. Marck, C. Neuvéglise, E. Talla, N. Goffard, L. Frangeul, M. Aigle, V. Anthouard, A. Babour, V. Barbe, S. Barnay, S. Blanchin, J.-M. Beckerich, E. Beyne, C. Bleykasten, A. Boisramé, J. Boyer, L. Cattolico, F. Confanioleri, A. de Daruvar, L. Despons, E. Fabre, C. Fairhead, H. Ferry-Dumazet, A. Groppi, F. Hantraye, C. Hennequin, N. Jauniaux, P. Joyet, R. Kachouri, A. Kerrest, R. Koszul, M. Lemaire, I. Lesur, L. Ma, H. Muller, J.-M. Nicaud, M. Nikolski, S. Oztas, O. Ozier-Kalogeropoulos, S. Pellenz, S. Potier, G.-F. Richard, M.-L. Straub, A. Suleau, D. Swennen, F. Tekaia, M. Wésolowski-Louvel, E. Westhof, B. Wirth, M. Zeniou-Meyer, I. Zivanovic, M. Bolotin-Fukuhara, A. Thierry, C. Bouchier, B. Caudron, C. Scarpelli, C. Gaillardin, J. Weissenbach, P. Wincker and J.-L. Souciet. Genome evolution in yeasts. Nature 430:35-44.
-
-
-
-
12
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
-
(1994)
Mol. Biol. Evol
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
13
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa, M., H. Kishino, and T. Yano. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-174.
-
(1985)
J. Mol. Evol
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
14
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D. T., W. R. Taylor, and J. M. Thornton. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:275-282.
-
(1992)
Comput. Appl. Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
16
-
-
34547675965
-
An empirical codon model for protein sequence evolution
-
Kosiol, C., I. Holmes, and N. Goldman. 2007. An empirical codon model for protein sequence evolution. Mol. Biol. Evol. 24:1464-1479.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1464-1479
-
-
Kosiol, C.1
Holmes, I.2
Goldman, N.3
-
17
-
-
0029973860
-
Synonymous nucleotide divergence: What is saturation?
-
Maynard Smith, J., and N.H. Smith. 1996. Synonymous nucleotide divergence: What is saturation? Genetics 142:1033-1036.
-
(1996)
Genetics
, vol.142
, pp. 1033-1036
-
-
Maynard Smith, J.1
Smith, N.H.2
-
18
-
-
0026428610
-
Adaptive protein evolution at the Adh locus in Drosophila
-
McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351:652-654.
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
19
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome
-
Muse, S. V., and B. S. Gaut 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
-
(1994)
Mol. Biol. Evol
, vol.11
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
20
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
-
(1986)
Mol. Biol. Evol
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
21
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen, R., and Z. Yang. 1998. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.2
-
22
-
-
0141721417
-
Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla
-
Nikaido, M., Y. Cao, M. Harada, N. Okada, and M. Hasegawa. 2003. Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla. Mol. Phylogenet. Evol. 28:276-284.
-
(2003)
Mol. Phylogenet. Evol
, vol.28
, pp. 276-284
-
-
Nikaido, M.1
Cao, Y.2
Harada, M.3
Okada, N.4
Hasegawa, M.5
-
23
-
-
0026870245
-
Gene conversion generates hypervariability at the variable regions of Kallikreins and their inhibitors
-
Ohta, T., and C. J. Basten. 1992. Gene conversion generates hypervariability at the variable regions of Kallikreins and their inhibitors. Mol. Phylgenet. Evol. 1:87-90.
-
(1992)
Mol. Phylgenet. Evol
, vol.1
, pp. 87-90
-
-
Ohta, T.1
Basten, C.J.2
-
24
-
-
31344433677
-
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction
-
Ren, F., H. Tanaka, and Z. Yang. 2005. An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst. Biol. 54:808-818.
-
(2005)
Syst. Biol
, vol.54
, pp. 808-818
-
-
Ren, F.1
Tanaka, H.2
Yang, Z.3
-
25
-
-
1542642309
-
Protein evolution with dependence among codons due to tertiary structure
-
Robinson, D. M., D. T. Jones, H. Kishino, N. Goldman, and J. L. Thorne. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol. 20:1692-1704.
-
(2003)
Mol. Biol. Evol
, vol.20
, pp. 1692-1704
-
-
Robinson, D.M.1
Jones, D.T.2
Kishino, H.3
Goldman, N.4
Thorne, J.L.5
-
26
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
27
-
-
0000120766
-
Estimating the dimension of a model
-
Schwarz, G. 1974. Estimating the dimension of a model. Ann. Stat. 6:461-464.
-
(1974)
Ann. Stat
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
28
-
-
84907319426
-
Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions
-
Self, S. G., and K.-L. Liang. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J. Am. Stat. Assoc. 82:605-610.
-
(1987)
J. Am. Stat. Assoc
, vol.82
, pp. 605-610
-
-
Self, S.G.1
Liang, K.-L.2
-
29
-
-
3042548848
-
Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences
-
Seo, T.-K., H. Kishino, and J. L. Thorne. 2004. Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences. Mol. Biol. Evol. 21:1201-1213.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1201-1213
-
-
Seo, T.-K.1
Kishino, H.2
Thorne, J.L.3
-
30
-
-
0003477556
-
-
5th edition, Edward Arnold, London, UK
-
Stuart, A., and K. Ord. 1996. Kendall's advanced theory of statistics, 5th edition, Volume 2. Edward Arnold, London, UK.
-
(1996)
Kendall's advanced theory of statistics
, vol.2
-
-
Stuart, A.1
Ord, K.2
-
31
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-1657.
-
(1998)
Mol. Biol. Evol
, vol.15
, pp. 1647-1657
-
-
Thorne, J.L.1
Kishino, H.2
Painter, I.S.3
-
32
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan, S., and N. Goldman. 2001. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18:691-699.
-
(2001)
Mol. Biol. Evol
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
33
-
-
4644373240
-
Estimating the frequency of events that cause multiple-nucleotide changes
-
Whelan, S., and N. Goldman. 2004. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics 167:2027-2043.
-
(2004)
Genetics
, vol.167
, pp. 2027-2043
-
-
Whelan, S.1
Goldman, N.2
-
34
-
-
3142739466
-
Detecting selection in noncoding regions of nucleotide sequences
-
Wong, W. S. W., and R. Nielsen. 2004. Detecting selection in noncoding regions of nucleotide sequences. Genetics 167:949-958.
-
(2004)
Genetics
, vol.167
, pp. 949-958
-
-
Wong, W.S.W.1
Nielsen, R.2
-
35
-
-
0033709702
-
Molecular evolution of cytochrome c oxidase subunit I in primates: Is there coevolution between mitochondrial and nuclear genomes?
-
Wu, W., T. R. Schmidt, M. Goodman, and L. I. Grossman. 2000. Molecular evolution of cytochrome c oxidase subunit I in primates: Is there coevolution between mitochondrial and nuclear genomes? Mol. Phylogenet. Evol. 17:294-304.
-
(2000)
Mol. Phylogenet. Evol
, vol.17
, pp. 294-304
-
-
Wu, W.1
Schmidt, T.R.2
Goodman, M.3
Grossman, L.I.4
-
36
-
-
0033639150
-
Statistical methods for detecting molecular adaptation?
-
Yang, Z., and J. P. Bielawski. 2000. Statistical methods for detecting molecular adaptation? Trends Ecol. Evol. 15:496-503.
-
(2000)
Trends Ecol. Evol
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
37
-
-
0031960185
-
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
-
Yang, Z., and R. Nielsen. 1998. Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46:409-418.
-
(1998)
J. Mol. Evol
, vol.46
, pp. 409-418
-
-
Yang, Z.1
Nielsen, R.2
-
38
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang, Z., and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 908-917
-
-
Yang, Z.1
Nielsen, R.2
-
39
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang, Z., R. Nielsen, N. Goldman, and A. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.K.4
-
40
-
-
0031792828
-
Models of amino acid substitution and applications to mitochondrial protein evolution
-
Yang, Z., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15:1600-1611.
-
(1998)
Mol. Biol. Evol
, vol.15
, pp. 1600-1611
-
-
Yang, Z.1
Nielsen, R.2
Hasegawa, M.3
|