-
1
-
-
84972510219
-
Statistical analysis of hominoid molecular evolution
-
Barry, D., Hartigan, J.A. 1987. Statistical analysis of hominoid molecular evolution. Stat. Sci. 2: 191-210.
-
(1987)
Stat. Sci
, vol.2
, pp. 191-210
-
-
Barry, D.1
Hartigan, J.A.2
-
2
-
-
47249122561
-
A site-and time-heterogeneous model of amino-acid replacement
-
Blanquart, S., Lartillot, N. 2008. A site-and time-heterogeneous model of amino-acid replacement. Mol. Biol. Evol. 25: 842-858
-
(2008)
Mol. Biol. Evol
, vol.25
, pp. 842-858
-
-
Blanquart, S.1
Lartillot, N.2
-
3
-
-
57749185463
-
Parallel adaptations to high temperatures in the Archaean eon
-
Boussau, B. Blanquart, A., Necsulea, A., Lartillot, N., Gouy, M. 2008. Parallel adaptations to high temperatures in the Archaean eon. Nature 456: 942-946.
-
(2008)
Nature
, vol.456
, pp. 942-946
-
-
Boussau Blanquart B, A.1
Necsulea, A.2
Lartillot, N.3
Gouy, M.4
-
4
-
-
35248857403
-
Efficient likelihood computations with non-reversible models of evolution
-
Boussau, B., Gouy, M. 2006. Efficient likelihood computations with non-reversible models of evolution. Syst. Biol. 55: 756-768.
-
(2006)
Syst. Biol
, vol.55
, pp. 756-768
-
-
Boussau, B.1
Gouy, M.2
-
5
-
-
5044244494
-
Anovel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor
-
Brooks, D.J., Fresco, J.R., Singh, M. 2004.Anovel method for estimating ancestral amino acid composition and its application to proteins of the Last Universal Ancestor. Bioinformatics 20: 2251-2257.
-
(2004)
Bioinformatics
, vol.20
, pp. 2251-2257
-
-
Brooks, D.J.1
Fresco, J.R.2
Singh, M.3
-
6
-
-
0027979994
-
Phylogeny of Greya (Lepidoptera: Pdoxidae), based on nucleotide sequence variation in mitochondrial Cytochrome Oxidase i and II: Congruence with morphological data
-
Brown, J.M., Pellmyr, O., Thompson, J.N., Harrison, R.G. 1994. Phylogeny of Greya (Lepidoptera: Pdoxidae), based on nucleotide sequence variation in mitochondrial Cytochrome Oxidase I and II: Congruence with morphological data. Mol. Biol. Evol. 11: 128-141.
-
(1994)
Mol. Biol. Evol
, vol.11
, pp. 128-141
-
-
Brown, J.M.1
Pellmyr, O.2
Thompson, J.N.3
Harrison, R.G.4
-
7
-
-
12044252488
-
Compositional bias, character state bias, and character-state reconstruction using parsimony
-
Collins, T.M., Wimberger, P.H., Naylor, G.J.P. 1994. Compositional bias, character state bias, and character-state reconstruction using parsimony. Syst. Biol. 43: 482-496.
-
(1994)
Syst. Biol
, vol.43
, pp. 482-496
-
-
Collins, T.M.1
Wimberger, P.H.2
Naylor, G.J.P.3
-
8
-
-
0002629270
-
Maximum likelihood from incomplete data via the em algorithm
-
Dempster,A.P., Laird,N.M., Rubin, D.B. 1977. Maximum likelihood from incomplete data via the EM algorithm. J. R. Statist. Soc. B, 39: 1-38.
-
(1977)
J. R. Statist. Soc. B
, vol.39
, pp. 1-38
-
-
Dempster, A.P.1
Laird, N.M.2
Rubin, D.B.3
-
9
-
-
0346104820
-
The universal ancestor and the ancestor of bacteria were hyperthermophiles
-
Di Giulio, M. 2003. The universal ancestor and the ancestor of bacteria were hyperthermophiles. J. Mol. Evol. 57: 721-730.
-
(2003)
J. Mol. Evol
, vol.57
, pp. 721-730
-
-
Di Giulio, M.1
-
10
-
-
0032434101
-
Problems with parsimony in sequences of biased base composition
-
Eyre-Walker,A. 1998. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47: 686-690.
-
(1998)
J. Mol. Evol
, vol.47
, pp. 686-690
-
-
Eyre-Walkera1
-
11
-
-
38949093003
-
Palaeotemperature trend for Precambrian life inferred from resurrected proteins
-
Gaucher, E.A.,Govindarajan, S., Ganesh, O.K. 2008. Palaeotemperature trend for Precambrian life inferred from resurrected proteins. Nature 451: 704-708.
-
(2008)
Nature
, vol.451
, pp. 704-708
-
-
Gaucher, E.A.1
Govindarajan, S.2
Ganesh, O.K.3
-
12
-
-
0141828152
-
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
-
Gaucher, E.A., Thomson, J.M., Burgan, M.F., Benner, S.A. 2003. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425: 285-288.
-
(2003)
Nature
, vol.425
, pp. 285-288
-
-
Gaucher, E.A.1
Thomson, J.M.2
Burgan, M.F.3
Benner, S.A.4
-
13
-
-
0031829758
-
Inferring pattern and process: Maximumlikelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
-
Galtier, N., Gouy, M. 1998. Inferring pattern and process: Maximumlikelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15: 871-879.
-
(1998)
Mol. Biol. Evol
, vol.15
, pp. 871-879
-
-
Galtier, N.1
Gouy, M.2
-
14
-
-
0020317308
-
Patterns of nucleotide substitution in pseudogenes and functional genes
-
Gojobori, T., Li, W.-H., Graur, D. 1982. Patterns of nucleotide substitution in pseudogenes and functional genes. J. Mol. Evol. 18: 360-369.
-
(1982)
J. Mol. Evol
, vol.18
, pp. 360-369
-
-
Gojobori, T.1
Li, W.-H.2
Graur, D.3
-
15
-
-
0022376704
-
Dating the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa, M., Kishino, H., Yano, T. 1985. Dating 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
-
16
-
-
0035527347
-
Empirical and hierarchical Bayesian estimation of ancestral states
-
Huelsenbeck, J.P., Bollback, J.P. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50: 351-336.
-
(2001)
Syst. Biol
, vol.50
, pp. 351-336
-
-
Huelsenbeck, J.P.1
Bollback, J.P.2
-
17
-
-
85127045450
-
Estimation of phylogeny using a general Markov model
-
Jayaswal, V., Jermiin, L., Robinson, J. 2005. Estimation of phylogeny using a general Markov model. Evol. Bioinf. Online 1: 62-80.
-
(2005)
Evol. Bioinf. Online
, vol.1
, pp. 62-80
-
-
Jayaswal, V.1
Jermiin, L.2
Robinson, J.3
-
18
-
-
0003100767
-
The validity of posterior expansions based on Laplace's method
-
Geisser S., Hodges J.S., Press S.J., Zellner A., editors Amsterdam Elsevier
-
Kass, R.E., Tierney, L., Kadane, J.B. 1990. The validity of posterior expansions based on Laplace's method. In: Geisser S., Hodges J.S., Press S.J., Zellner A., editors. Bayesian and Likelihood Methods in Statistics and Econometrics. Amsterdam: Elsevier.
-
(1990)
Bayesian and Likelihood Methods in Statistics and Econometrics
-
-
Kass, R.E.1
Tierney, L.2
Kadane, J.B.3
-
19
-
-
4944223649
-
Ancestral sequence reconstruction in primate mitochondrial DNA: Compositional bias and effect on functional inference
-
Krishnan, N.M., Seligmann, H., Stewart, C.B., De Koning, A.P., Pollock, D.D. 2004. Ancestral sequence reconstruction in primate mitochondrial DNA: Compositional bias and effect on functional inference. Mol. Biol. Evol. 21: 1871-1883.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1871-1883
-
-
Krishnan, N.M.1
Seligmann, H.2
Stewart, C.B.3
De Koning, A.P.4
Pollock, D.D.5
-
20
-
-
0033422611
-
The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies
-
Pagel, M. 1999. The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies Syst. Biol. 48: 612-622.
-
(1999)
Syst. Biol.
, vol.48
, pp. 612-622
-
-
Pagel, M.1
-
21
-
-
36348992886
-
Dealing with uncertainty in ancestral sequence reconstruction: Sampling from the posterior distribution
-
Liberles, D.A. editor Oxford Univ. Press
-
Pollock, D.D., Chang, B.W. 2007. Dealing with uncertainty in ancestral sequence reconstruction: Sampling from the posterior distribution. In: Liberles, D.A. editor. Ancestral Sequence Recontruction. Oxford Univ. Press. 85-94.
-
(2007)
Ancestral Sequence Recontruction
, pp. 85-94
-
-
Pollock, D.D.1
Chang, B.W.2
-
22
-
-
0026711010
-
Estimation of the number of nucleotide substitutions when there are strong transitition-transversion and G+C-content biases
-
Tamura, K. 1992. Estimation of the number of nucleotide substitutions when there are strong transitition-transversion and G+C-content biases. Mol. Biol. Evol. 9: 678-687.
-
(1992)
Mol. Biol. Evol.
, vol.9
, pp. 678-687
-
-
Tamura, K.1
-
23
-
-
0000167944
-
Note on the consistency of the maximum likelihood estimate
-
Wald, A. 1949. Note on the consistency of the maximum likelihood estimate. Ann. Math. Statist. 20: 595-601.
-
(1949)
Ann. Math. Statist
, vol.20
, pp. 595-601
-
-
Wald, A.1
-
24
-
-
0002644952
-
Maximum likelihood estimation of misspecified models
-
White, H. 1982. Maximum likelihood estimation of misspecified models. Econometrica 50: 1-25.
-
(1982)
Econometrica
, vol.50
, pp. 1-25
-
-
White, H.1
-
25
-
-
33745605535
-
Assessing the accuracy of ancestral protein reconstruction methods
-
Williams, P.D., Pollock, D.P., Blackburne, B.P. and R.A. Goldstein 2006. Assessing the accuracy of ancestral protein reconstruction methods. PLOS Comput. Biol., 2: e69.
-
(2006)
PLOS Comput. Biol.
, vol.2
-
-
Williams, P.D.1
Pollock, D.P.2
Blackburne, B.P.3
Goldstein, R.A.4
-
26
-
-
0033858988
-
The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders
-
Schmitz, J., Ohme, M., Zischler, H. 2000. The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders. Biol. Evol. 17: 1334-1343.
-
(2000)
Biol. Evol.
, vol.17
, pp. 1334-1343
-
-
Schmitz, J.1
Ohme, M.2
Zischler, H.3
-
27
-
-
34547803197
-
PAML 4: A program for phylogenetic analysis by maximum likelihood
-
Yang, Z. 2007. PAML 4: A program for phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1586-1591
-
-
Yang, Z.1
-
29
-
-
0030683599
-
PAML: A program for phylogenetic analysis by maximum likelihood
-
Yang, Z. 1997. PAML: A program for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13: 555-556.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
30
-
-
33846519263
-
Protein and DNA sequence determinants of thermophilic adaptation
-
Zeldovich, K.B., Berezovsky, I.N., Shakhnovich, E.I. 2007. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput. Biol. 3: 62-72.
-
(2007)
PLoS Comput. Biol
, vol.3
, pp. 62-72
-
-
Zeldovich, K.B.1
Berezovsky, I.N.2
Shakhnovich, E.I.3
-
31
-
-
84868017921
-
Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the Barry-Hartigan model
-
in press doi: 10.1093/sysbio/sys046
-
Zou, L., Susko, E., Field, C., Roger, A.J. 2012. Fitting nonstationary general-time-reversible models to obtain edge-lengths and frequencies for the Barry-Hartigan model. Syst. Biol. (in press) doi: 10.1093/sysbio/sys046.
-
(2012)
Syst. Biol
-
-
Zou, L.1
Susko, E.2
Field, C.3
Roger, A.J.4
-
32
-
-
80054891334
-
The Barry and Hartigan general Markov model suffers from statistical non-identifiability
-
Zou, L., Field, C., Susko, E., Roger, A.J. 2011. The Barry and Hartigan general Markov model suffers from statistical non-identifiability. Syst. Biol. 60: 872-875.
-
(2011)
Syst. Biol
, vol.60
, pp. 872-875
-
-
Zou, L.1
Field, C.2
Susko, E.3
Roger, A.J.4
|