-
1
-
-
84555188616
-
BEAGLE: An application programming interface and highperformance computing library for statistical phylogenetics
-
Ayres, D.L. et al. (2012) BEAGLE: an application programming interface and highperformance computing library for statistical phylogenetics. Syst. Biol., 61, 170-173.
-
(2012)
Syst. Biol.
, vol.61
, pp. 170-173
-
-
Ayres, D.L.1
-
2
-
-
79957510431
-
Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes
-
Baele, G. et al. (2011) Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes. BMC Evol. Biol., 11, 145.
-
(2011)
BMC Evol. Biol
, vol.11
, pp. 145
-
-
Baele, G.1
-
3
-
-
84865475040
-
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty
-
Baele, G. et al. (2012) Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol. Biol. Evol., 29, 2157-2167.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 2157-2167
-
-
Baele, G.1
-
4
-
-
84877663836
-
Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics
-
Baele, G. et al. (2013a) Accurate model selection of relaxed molecular clocks in Bayesian phylogenetics. Mol. Biol. Evol., 30, 239-243.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 239-243
-
-
Baele, G.1
-
5
-
-
84874534890
-
Make the most of your samples: Bayes factor estimators for high-dimensional models of sequence evolution
-
Baele, G. et al. (2013b) Make the most of your samples: bayes factor estimators for high-dimensional models of sequence evolution. BMC Bioinformatics, 14, 85.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 85
-
-
Baele, G.1
-
6
-
-
34447253826
-
Accounting for gene rate heterogeneity in phylogenetic inference
-
Bevan, R.B. et al. (2007) Accounting for gene rate heterogeneity in phylogenetic inference. Syst. Biol., 56, 194-205.
-
(2007)
Syst. Biol.
, vol.56
, pp. 194-205
-
-
Bevan, R.B.1
-
7
-
-
12044257391
-
Partitioning and combining data in phylogenetic analysis
-
Bull, J.J. et al. (1993) Partitioning and combining data in phylogenetic analysis. Syst. Biol., 42, 384-397.
-
(1993)
Syst. Biol.
, vol.42
, pp. 384-397
-
-
Bull, J.J.1
-
8
-
-
84880467251
-
Graph hierarchies for phylogeography
-
Cybis, G.B. et al. (2013) Graph hierarchies for phylogeography. Phil. Trans. R. Soc. B, Biol. Sci., 368, 20120206.
-
(2013)
Phil. Trans. R. Soc. B, Biol. Sci.
, vol.368
, pp. 20120206
-
-
Cybis, G.B.1
-
9
-
-
33344465800
-
Relaxed phylogenetics and dating with confidence
-
Drummond, A.J. et al. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol., 4, e88.
-
(2006)
PLoS Biol.
, vol.4
-
-
Drummond, A.J.1
-
10
-
-
77956488734
-
Bayesian random local clocks, or one rate to rule them all
-
Drummond, A.J. and Suchard, M.A. (2010) Bayesian random local clocks, or one rate to rule them all. BMC Biology, 8, 114.
-
(2010)
BMC Biology
, vol.8
, pp. 114
-
-
Drummond, A.J.1
Suchard, M.A.2
-
11
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
Drummond, A.J. et al. (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol., 29, 1969-1973.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1969-1973
-
-
Drummond, A.J.1
-
12
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc, F. et al. (2005) Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet, 6, 361-375.
-
(2005)
Nat. Rev. Genet
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
-
13
-
-
79955417630
-
Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: Efficient hypothesis testing through hierarchical phylogenetic models
-
Edo-Matas, D. et al. (2011) Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models. Mol. Biol. Evol., 28, 1605-1616.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 1605-1616
-
-
Edo-Matas, D.1
-
14
-
-
0038518196
-
Phylogenomics: Intersection of evolution and genomics
-
Eisen, J.A. and Fraser, C.M. (2003) Phylogenomics: intersection of evolution and genomics. Science, 300, 1706-1707.
-
(2003)
Science
, vol.300
, pp. 1706-1707
-
-
Eisen, J.A.1
Fraser, C.M.2
-
15
-
-
0242318326
-
Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes
-
Faith, J.J. and Pollock, D.D. (2003) Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics, 165, 735-745.
-
(2003)
Genetics
, vol.165
, pp. 735-745
-
-
Faith, J.J.1
Pollock, D.D.2
-
16
-
-
42149143421
-
Marginal likelihood estimation via power posteriors
-
Friel, N. and Petitt, A.N. (2008) Marginal likelihood estimation via power posteriors. J. R. Stat. Soc. B., 70, 589-607.
-
(2008)
J. R. Stat. Soc. B.
, vol.70
, pp. 589-607
-
-
Friel, N.1
Petitt, A.N.2
-
17
-
-
48049107322
-
The conditioned reconstructed process
-
Gernhard, T. (2008) The conditioned reconstructed process. J. Theor. Biol., 253, 769-778.
-
(2008)
J. Theor. Biol.
, vol.253
, pp. 769-778
-
-
Gernhard, T.1
-
18
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein coding DNA sequences
-
Goldman, N. and Yang, Z.H. (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.H.2
-
19
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa, M. et al. (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
-
20
-
-
33645850710
-
Phylogenomics: The beginning of incongruence?
-
Jeffroy, O. et al. (2006) Phylogenomics: the beginning of incongruence? Trends Genet., 22, 225-231.
-
(2006)
Trends Genet.
, vol.22
, pp. 225-231
-
-
Jeffroy, O.1
-
21
-
-
0000732090
-
Evolution of protein molecules
-
Munro, H.M. (ed.), Academic Press, New York
-
Jukes, T.H. and Cantor, C.R. (1969) Evolution of protein molecules. In: Munro, H.M. (ed.) Mammalian protein metabolism. Academic Press, New York, pp. 21-132.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
22
-
-
27844569825
-
Site-to-site variation of synonymous substitution rates
-
Kosakovsky Pond, S.L. and Muse, S. (2005) Site-to-site variation of synonymous substitution rates. Mol. Biol. Evol., 22, 2375-2385.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 2375-2385
-
-
Kosakovsky Pond, S.L.1
Muse, S.2
-
23
-
-
84862928655
-
Statistics and truth in phylogenomics
-
Kumar, S. et al. (2012) Statistics and truth in phylogenomics. Mol. Biol. Evol., 29, 457-472.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 457-472
-
-
Kumar, S.1
-
24
-
-
33644826560
-
Computing Bayes factors using thermodynamic integration
-
Lartillot, N. and Philippe, H. (2006) Computing Bayes factors using thermodynamic integration. Syst. Biol., 55, 195-207.
-
(2006)
Syst. Biol.
, vol.55
, pp. 195-207
-
-
Lartillot, N.1
Philippe, H.2
-
25
-
-
84870797333
-
A counting renaissance: Combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
-
Lemey, P. et al. (2012) A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection. Bioinformatics, 28, 3248-3256.
-
(2012)
Bioinformatics
, vol.28
, pp. 3248-3256
-
-
Lemey, P.1
-
26
-
-
0028024626
-
A likelihood approach for comparing synonymous and non-synonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse, S.V. and Gaut, B.S. (1994) A likelihood approach for comparing synonymous and non-synonymous 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
-
27
-
-
38349192060
-
Strong variations of mitochondrial mutation rate across mammals - The longevity hypothesis
-
Nabholz, B. et al. (2008) Strong variations of mitochondrial mutation rate across mammals - the longevity hypothesis. Mol. Biol. Evol., 25, 120-130.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 120-130
-
-
Nabholz, B.1
-
28
-
-
0003078723
-
Approximating Bayesian inference with the weigthed likelihood bootstrap
-
Newton, M.A. and Raftery, A.E. (1994) Approximating Bayesian inference with the weigthed likelihood bootstrap. J. R. Stat. Soc. B, 56, 3-48.
-
(1994)
J. R. Stat. Soc. B
, vol.56
, pp. 3-48
-
-
Newton, M.A.1
Raftery, A.E.2
-
29
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen, R. and Yang, Z.H. (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.H.2
-
30
-
-
1642341403
-
Bayesian phylogenetic analysis of combined data
-
Nylander, J.A. et al. (2004) Bayesian phylogenetic analysis of combined data. Syst. Biol., 53, 47-67.
-
(2004)
Syst. Biol.
, vol.53
, pp. 47-67
-
-
Nylander, J.A.1
-
31
-
-
0031950474
-
Asymmetrical directional mutation pressure in the mitochondrial genome of mammals
-
Reyes, A. et al. (1998) Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. Mol. Biol. Evol., 15, 957-966.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 957-966
-
-
Reyes, A.1
-
32
-
-
58449095670
-
Bayesian comparisons of codon substitution models
-
Rodrigue, N. et al. (2008) Bayesian comparisons of codon substitution models. Genetics, 180, 1579-1591.
-
(2008)
Genetics
, vol.180
, pp. 1579-1591
-
-
Rodrigue, N.1
-
33
-
-
81855168357
-
Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection
-
Rubinstein, N.D. et al. (2011) Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection. Mol. Biol. Evol., 28, 3297-3308.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 3297-3308
-
-
Rubinstein, N.D.1
-
34
-
-
28944450584
-
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
-
Shapiro, B. et al. (2006) Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol. Biol. Evol., 23, 7-9.
-
(2006)
Mol. Biol. Evol.
, vol.23
, pp. 7-9
-
-
Shapiro, B.1
-
35
-
-
65649118549
-
Many-core algorithms for statistical phylogenetics
-
Suchard, M.A. and Rambaut, A. (2009) Many-core algorithms for statistical phylogenetics. Bioinformatic, 25, 1370-1376.
-
(2009)
Bioinformatic
, vol.25
, pp. 1370-1376
-
-
Suchard, M.A.1
Rambaut, A.2
-
36
-
-
0242404116
-
Hierarchical phylogenetic models for analyzing multipartite sequence data
-
Suchard, M.A. et al. (2003) Hierarchical phylogenetic models for analyzing multipartite sequence data. Syst. Biol., 52, 649-664.
-
(2003)
Syst. Biol.
, vol.52
, pp. 649-664
-
-
Suchard, M.A.1
-
37
-
-
0002671410
-
Some probabilistic and statistical problems in the analysis of DNA sequences
-
Waterman, M.S. (ed.), AmericanMathematical Society, Providence (RI)
-
Tavaré, S. (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. In: Waterman, M.S. (ed.) Some Mathematical Questions in Biology: DNA Sequence Analysis. AmericanMathematical Society, Providence (RI), pp. 57-86.
-
(1986)
Some Mathematical Questions in Biology: DNA Sequence Analysis
, pp. 57-86
-
-
Tavaré, S.1
-
38
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
Thorne, J.L. et al. (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
-
40
-
-
79951566251
-
Improving marginal likelihood estimation for Bayesian phylogenetic model selection
-
Xie, W. et al. (2011) Improving marginal likelihood estimation for Bayesian phylogenetic model selection. Syst. Biol., 60, 150-160.
-
(2011)
Syst. Biol.
, vol.60
, pp. 150-160
-
-
Xie, W.1
-
41
-
-
0030451420
-
Among-site rate variation and its impact on phylogenetic analyses
-
Yang, Z. (1996a) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol., 11, 367-372.
-
(1996)
Trends Ecol. Evol.
, vol.11
, pp. 367-372
-
-
Yang, Z.1
-
42
-
-
0029970097
-
Maximum-likelihood models for combined analyses of multiple sequence data
-
Yang, Z. (1996b) Maximum-likelihood models for combined analyses of multiple sequence data. J. Mol. Evol., 42, 587-596.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 587-596
-
-
Yang, Z.1
-
43
-
-
0031897964
-
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
-
Yang, Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol., 15, 568-573.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 568-573
-
-
Yang, Z.1
|