-
1
-
-
53849139154
-
Wagner and Dollo: A stochastic duet by composing two parsimonious solos
-
Alekseyenko A., Lee C., Suchard M. 2008. Wagner and Dollo: a stochastic duet by composing two parsimonious solos. Syst. Biol. 57:772-784.
-
(2008)
Syst. Biol
, vol.57
, pp. 772-784
-
-
Alekseyenko, A.1
Lee, C.2
Suchard, M.3
-
2
-
-
53849128927
-
A model-based approach to study nearest-neighbor infuences reveals complex substitution patterns in non-coding sequences
-
Baele G., Peer Y.V., Vansteelandt S. 2008. A model-based approach to study nearest-neighbor infuences reveals complex substitution patterns in non-coding sequences. Syst. Biol. 57:675-692.
-
(2008)
Syst. Biol
, vol.57
, pp. 675-692
-
-
Baele, G.1
Peer, Y.V.2
Vansteelandt, S.3
-
3
-
-
34547812067
-
Mitochondrial genome and nuclear sequence data support Myzostomida as part of the annelid radiation
-
DOI 10.1093/molbev/msm086
-
Bleidorn C., Eeckhaut I., Podsiadlowski L., Schults N., McHugh D., Halanych K., Milinkovitch M., Tiedemann R. 2007. Mitochondrial genome and nuclear sequence data support Myzostomida as part of the annelid radiation. Mol. Biol. Evol. 24:1690-1701. (Pubitemid 47236686)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1690-1701
-
-
Bleidorn, C.1
Eeckhaut, I.2
Podsiadlowski, L.3
Schult, N.4
McHugh, D.5
Halanych, K.M.6
Milinkovitch, M.C.7
Tiedemann, R.8
-
4
-
-
33645024781
-
Posterior mapping and posterior predictive distributions
-
Nielsen R., editor New York: Springer
-
Bollback J.P. 2005. Posterior mapping and posterior predictive distributions. In: Nielsen R., editor. Statistical methods in molecular evolution. New York: Springer. p. 439-462.
-
(2005)
Statistical Methods in Molecular Evolution
, pp. 439-462
-
-
Bollback, J.P.1
-
5
-
-
37249003697
-
The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics
-
Brown J., Lemmon A. 2007. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Syst. Biol. 56:643-655.
-
(2007)
Syst. Biol
, vol.56
, pp. 643-655
-
-
Brown, J.1
Lemmon, A.2
-
6
-
-
74549220350
-
Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories
-
de Koning J.A.P., Gu W., Pollock D.D. 2010. Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Mol. Biol. Evol. 27:249-265.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 249-265
-
-
De Koning, J.A.P.1
Gu, W.2
Pollock, D.D.3
-
7
-
-
38649110663
-
BEAST: Bayesian evolutionary analysis by sampling trees
-
Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
-
(2007)
BMC Evol. Biol
, vol.7
, pp. 214
-
-
Drummond, A.J.1
Rambaut, A.2
-
8
-
-
78650500247
-
Choosing among partition models in Bayesian phylogenetics
-
Fan Y., Wu R., Chen M.-H., Kuo L., Lewis P.O. 2011. Choosing among partition models in Bayesian phylogenetics. Mol. Biol. Evol. 28: 523-532.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 523-532
-
-
Fan, Y.1
Wu, R.2
Chen, M.-H.3
Kuo, L.4
Lewis, P.O.5
-
9
-
-
77956889087
-
Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
-
Green P.J. 1995. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika. 82: 711-732.
-
(1995)
Biometrika
, vol.82
, pp. 711-732
-
-
Green, P.J.1
-
10
-
-
0031875569
-
Evolutionary distances for protein-coding sequences: Modeling site- specific residue frequencies
-
Halpern A.L., Bruno W.J. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol. Biol. Evol. 15:910-917. (Pubitemid 28321889)
-
(1998)
Molecular Biology and Evolution
, vol.15
, Issue.7
, pp. 910-917
-
-
Halpern, A.L.1
Bruno, W.J.2
-
11
-
-
62649113993
-
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"
-
Hampl V., Hug L., Leigh J.W., Dacks J.B., Lang B.F., Simpson A.G.B., Roger A. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc. Natl. Acad. Sci. U. S. A. 106:3859-3864.
-
(2009)
Proc. Natl. Acad. Sci. U. S. A
, vol.106
, pp. 3859-3864
-
-
Hampl, V.1
Hug, L.2
Leigh, J.W.3
Dacks, J.B.4
Lang, B.F.5
Simpson, A.G.B.6
Roger, A.7
-
12
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
Hastings W.K. 1970. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 57:97-109.
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.K.1
-
13
-
-
2442671519
-
Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
-
DOI 10.1093/molbev/msh123
-
Huelsenbeck J.P., Larget B., Alfaro M.E. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123-1133. (Pubitemid 38658220)
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.6
, pp. 1123-1133
-
-
Huelsenbeck, J.P.1
Larget, B.2
Alfaro, M.E.3
-
14
-
-
33846432342
-
Some tests of significance, treated by the theory of probability
-
Jeffreys H. 1935. Some tests of significance, treated by the theory of probability. Proc. Camb. Philos. Soc. 31:203-222.
-
(1935)
Proc. Camb. Philos. Soc
, vol.31
, pp. 203-222
-
-
Jeffreys, H.1
-
15
-
-
84950934893
-
Bayes factors and model uncertainty
-
Kass R., Raftery A. 1995. Bayes factors and model uncertainty. J. Am. Stat. Assoc. 90:773-795.
-
(1995)
J. Am. Stat. Assoc
, vol.90
, pp. 773-795
-
-
Kass, R.1
Raftery, A.2
-
16
-
-
33846593309
-
Conjugate Gibbs sampling for Bayesian phylogenetic models
-
DOI 10.1089/cmb.2006.13.1701
-
Lartillot N. 2006. Conjugate Gibbs sampling for Bayesian phylogenetic models. J. Comput. Biol. 13:1701-1722. (Pubitemid 46175705)
-
(2006)
Journal of Computational Biology
, vol.13
, Issue.10
, pp. 1701-1722
-
-
Lartillot, N.1
-
17
-
-
33644826560
-
Computing Bayes factors using thermodynamic integration
-
DOI 10.1080/10635150500433722, PII G4465276345678
-
Lartillot N., Philippe H. 2006. Computing Bayes factors using thermo-dynamic integration. Syst. Biol. 55:195-207. (Pubitemid 43355101)
-
(2006)
Systematic Biology
, vol.55
, Issue.2
, pp. 195-207
-
-
Lartillot, N.1
Philippe, H.2
-
18
-
-
53749090508
-
Empirical profile mixture models for phylogenetic reconstruction
-
Le, S.Q., Gascuel O., Lartillot N. 2008. Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics. 24: 2317-2323.
-
(2008)
Bioinformatics
, vol.24
, pp. 2317-2323
-
-
Le, S.Q.1
Gascuel, O.2
Lartillot, N.3
-
19
-
-
33744982664
-
Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation
-
Mateiu L., Rannala B. 2006. Inferring complex DNA substitution processes on phylogenies using uniformization and data augmentation. Syst. Biol. 55:259-269.
-
(2006)
Syst. Biol
, vol.55
, pp. 259-269
-
-
Mateiu, L.1
Rannala, B.2
-
20
-
-
5744249209
-
Equation of state calculation by fast computing machines
-
Metropolis S., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., Teller E. 1953. Equation of state calculation by fast computing machines. J. Chem. Phys. 21:1087-1092.
-
(1953)
J. Chem. Phys
, vol.21
, pp. 1087-1092
-
-
Metropolis, S.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
21
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse S.V., Gaut B.S. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitutions, with applications to chloroplast genome. Mol. Biol. Evol. 11:715-724. (Pubitemid 24274880)
-
(1994)
Molecular Biology and Evolution
, vol.11
, Issue.5
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
22
-
-
0003078723
-
Approximating Bayesian inference with the weighted likelihood bootstrap
-
Newton M.A., Raftery A.E. 1994. Approximating Bayesian inference with the weighted 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
-
23
-
-
0036804625
-
Mapping mutations on phylogenies
-
DOI 10.1080/10635150290102393
-
Nielsen R. 2002. Mapping mutations on phylogenies. Syst. Biol. 51: 729-739. (Pubitemid 35294805)
-
(2002)
Systematic Biology
, vol.51
, Issue.5
, pp. 729-739
-
-
Nielsen, R.1
-
24
-
-
0035035443
-
A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames
-
Pedersen A.-M.K., Jensen J.L. 2001. A dependent rates model and MCMC based methodology for the maximum likelihood analysis of sequences with overlapping reading frames. Mol. Biol. Evol. 18:763-776. (Pubitemid 32372947)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.5
, pp. 763-776
-
-
Pedersen, A.-M.K.1
Jensen, J.L.2
-
25
-
-
52249108078
-
Phylogeny and biogeography of bees and the tribe Osmiini (Hy-menoptera: Megachilidae)
-
Praz C., Muller A., Danforth B., Griswold T., Widmer A., Dorn S. 2008. Phylogeny and biogeography of bees and the tribe Osmiini (Hy-menoptera: Megachilidae). Mol. Phylogenet. Evol. 49:185-197.
-
(2008)
Mol. Phylogenet. Evol
, vol.49
, pp. 185-197
-
-
Praz, C.1
Muller, A.2
Danforth, B.3
Griswold, T.4
Widmer, A.5
Dorn, S.6
-
26
-
-
1542642309
-
Protein evolution with dependence among codons due to tertiary structure
-
DOI 10.1093/molbev/msg184
-
Robinson D.M., Jones D.T., Kishino H., Goldman N., Thorne J.L. 2003. Protein evolution with dependence among codons due to tertiary structure. Mol. Biol. Evol. 20:1692-1704. (Pubitemid 41070832)
-
(2003)
Molecular Biology and Evolution
, vol.20
, Issue.10
, pp. 1692-1704
-
-
Robinson, D.M.1
Jones, D.T.2
Kishino, H.3
Goldman, N.4
Thorne, J.L.5
-
27
-
-
67649329427
-
Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codon
-
Rodrigue N., Kleinman C., Philippe H., Lartillot N. 2009. Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codon. Mol. Biol. Evol. 26:1663-1676.
-
(2009)
Mol. Biol. Evol
, vol.26
, pp. 1663-1676
-
-
Rodrigue, N.1
Kleinman, C.2
Philippe, H.3
Lartillot, N.4
-
28
-
-
33748126145
-
Assessing site-interdependent phylogenetic models of sequence evolution
-
DOI 10.1093/molbev/msl041
-
Rodrigue N., Philippe H., Lartillot N. 2006. Assessing site-interdependent phylogenetic models of sequence evolution. Mol. Biol. Evol. 23:1762-1775. (Pubitemid 44309770)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.9
, pp. 1762-1775
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
29
-
-
34548630641
-
Exploring fast computational strategies for probabilistic phylogenetic analysis
-
DOI 10.1080/10635150701611258, PII 781937249
-
Rodrigue N., Philippe H., Lartillot N. 2007. Exploring fast computational strategies for probabilistic phylogenetic analysis. Syst. Biol. 56:711-726. (Pubitemid 47402905)
-
(2007)
Systematic Biology
, vol.56
, Issue.5
, pp. 711-726
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
30
-
-
58449095670
-
Bayesian comparisons of codon substitution models
-
Rodrigue N., Philippe H., Lartillot N. 2008a. Bayesian comparisons of codon substitution models. Genetics. 180:1579-1591.
-
(2008)
Genetics
, vol.180
, pp. 1579-1591
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
31
-
-
37549005159
-
Uniformization for sampling realizations of Markov processes: Applications to Bayesian implementations of codon substitution models
-
Rodrigue N., Philippe H., Lartillot N. 2008b. Uniformization for sampling realizations of Markov processes: applications to Bayesian implementations of codon substitution models. Bioinformatics. 24:56-62.
-
(2008)
Bioinformatics
, vol.24
, pp. 56-62
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
32
-
-
77949536563
-
Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid ftness profiles
-
Rodrigue N., Philippe H., Lartillot N. 2010. Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid ftness profiles. Proc. Natl. Acad. Sci. U. S. A. 107:4629-4634.
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, pp. 4629-4634
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
33
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
DOI 10.1093/bioinformatics/btg180
-
Ronquist F., Huelsenbeck J.P. 2003. Mrbayes 3: Bayesian phy-logenetic inference under mixed models. Bioinformatics. 19: 1572-1574. (Pubitemid 37038874)
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
35
-
-
65649118549
-
Many-core algorithms for statistical phylogenetics
-
Suchard M.A., Rambaut A. 2009. Many-core algorithms for statistical phylogenetics. Bioinformatics. 25:1370-1376.
-
(2009)
Bioinformatics
, vol.25
, pp. 1370-1376
-
-
Suchard, M.A.1
Rambaut, A.2
-
36
-
-
21844487977
-
Computing Bayes factors using a generalization of the Savage-Dickey density ratio
-
Verdinelli I., Wasserman L. 1995. Computing Bayes factors using a generalization of the Savage-Dickey density ratio. J. Am. Stat. Assoc. 90:614-618.
-
(1995)
J. Am. Stat. Assoc
, vol.90
, pp. 614-618
-
-
Verdinelli, I.1
Wasserman, L.2
-
37
-
-
79951566251
-
Improving marginal likelihood estimation for Bayesian phylogenetic model selection
-
Xie W., Lewis P.O., Fan Y., Kuo L., Chen M.-H. 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
Lewis, P.O.2
Fan, Y.3
Kuo, L.4
Chen, M.-H.5
-
38
-
-
39749161509
-
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
-
DOI 10.1093/molbev/msm284
-
Yang Z., Nielsen R. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol. Biol. Evol. 25:568-579. (Pubitemid 351301912)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.3
, pp. 568-579
-
-
Yang, Z.1
Nielsen, R.2
-
39
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang Z., Nielsen R., Goldman N., Pedersen A.-M.K. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155:431-449. (Pubitemid 30257141)
-
(2000)
Genetics
, vol.155
, Issue.1
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.-M.K.4
|