-
1
-
-
84857198898
-
A dirichlet process prior for estimating lineage-specific substitution rates
-
T. A. Heath, M. T. Holder, and J. P. Huelsenbeck, "A dirichlet process prior for estimating lineage-specific substitution rates," Molecular Biology and Evolution, vol. 29, no. 3, pp. 939-955, 2012. [Online]. Available: http://mbe.oxfordjournals.org/content/29/3/939.abstract
-
(2012)
Molecular Biology and Evolution
, vol.29
, Issue.3
, pp. 939-955
-
-
Heath, T.A.1
Holder, M.T.2
Huelsenbeck, J.P.3
-
2
-
-
84865256173
-
A hierarchical Bayesian model for calibrating estimates of species divergence times
-
T. A. Heath, "A hierarchical Bayesian model for calibrating estimates of species divergence times," Systematic Biology, vol. 61, pp. 793-809, 2012.
-
(2012)
Systematic Biology
, vol.61
, pp. 793-809
-
-
Heath, T.A.1
-
3
-
-
0001120413
-
A Bayesian analysis of some nonparametric problems
-
T. S. Ferguson, "A Bayesian analysis of some nonparametric problems," Annals of Statistics, vol. 1, pp. 209-230, 1973.
-
(1973)
Annals of Statistics
, vol.1
, pp. 209-230
-
-
Ferguson, T.S.1
-
4
-
-
0000708831
-
Mixtures of Dirichlet processes with applications to non-parametric problems
-
C. E. Antoniak, "Mixtures of Dirichlet processes with applications to non-parametric problems," Annals of Statistics, vol. 2, pp. 1152-1174, 1974.
-
(1974)
Annals of Statistics
, vol.2
, pp. 1152-1174
-
-
Antoniak, C.E.1
-
5
-
-
0002331493
-
Molecular disease, evolution, and genetic heterogeneity
-
M. Kasha and B. Pullman, Eds. Academic Press, New York
-
E. Zuckerkandl and L. Pauling, "Molecular disease, evolution, and genetic heterogeneity," in Horizons in Biochemistry, M. Kasha and B. Pullman, Eds. Academic Press, New York, 1962, pp. 189-225.
-
(1962)
Horizons in Biochemistry
, pp. 189-225
-
-
Zuckerkandl, E.1
Pauling, L.2
-
6
-
-
0242571576
-
Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species
-
Z. Yang and A. D. Yoder, "Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species," Systematic Biology, vol. 52, pp. 705-716, 2003.
-
(2003)
Systematic Biology
, vol.52
, pp. 705-716
-
-
Yang, Z.1
Yoder, A.D.2
-
7
-
-
77956488734
-
Bayesian random local clocks, or one rate to rule them all
-
A. J. Drummond and M. A. Suchard, "Bayesian random local clocks, or one rate to rule them all," BMC Biology, vol. 8, p. 114, 2010.
-
(2010)
BMC Biology
, vol.8
, pp. 114
-
-
Drummond, A.J.1
Suchard, M.A.2
-
8
-
-
33344465800
-
Relaxed phylogenetics and dating with confidence
-
A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, "Relaxed phylogenetics and dating with confidence," PLoS Biology, vol. 4, p. e88, 2006.
-
(2006)
PLoS Biology
, vol.4
-
-
Drummond, A.J.1
Ho, S.Y.2
Phillips, M.J.3
Rambaut, A.4
-
9
-
-
37549001784
-
A general comparison of relaxed molecular clock models
-
T. Lepage, D. Bryant, H. Philippe, and N. Lartillot, "A general comparison of relaxed molecular clock models," Molecular Biology and Evolution, vol. 24, pp. 2669-2680, 2007.
-
(2007)
Molecular Biology and Evolution
, vol.24
, pp. 2669-2680
-
-
Lepage, T.1
Bryant, D.2
Philippe, H.3
Lartillot, N.4
-
10
-
-
77950032550
-
Markov chain sampling methods for Dirichlet process mixture models
-
R. M. Neal, "Markov chain sampling methods for Dirichlet process mixture models," Journal of Computational and Graphical Statistics, vol. 9, pp. 249-265, 2000.
-
(2000)
Journal of Computational and Graphical Statistics
, vol.9
, pp. 249-265
-
-
Neal, R.M.1
-
11
-
-
33750403801
-
RAxML-VI-HPC: Maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models
-
A. Stamatakis, "RAxML-VI-HPC: maximum likelihoodbased phylogenetic analyses with thousands of taxa and mixed models," Bioinformatics, vol. 22, no. 21, pp. 2688-2690, 2006.
-
(2006)
Bioinformatics
, vol.22
, Issue.21
, pp. 2688-2690
-
-
Stamatakis, A.1
-
12
-
-
0036135468
-
Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
-
M. J. Sanderson, "Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach," Molecular Biology and Evolution, vol. 19, pp. 101-109, 2002.
-
(2002)
Molecular Biology and Evolution
, vol.19
, pp. 101-109
-
-
Sanderson, M.J.1
-
13
-
-
0037314098
-
R8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
-
M. J. Sanderson, "r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock," Bioinformatics, vol. 19, no. 2, pp. 301-302, 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 301-302
-
-
Sanderson, M.J.1
-
14
-
-
84870458929
-
Treepl: Divergence time estimation using penalized likelihood for large phylogenies
-
2012
-
S. A. Smith and B. C. O'Meara, "treepl: divergence time estimation using penalized likelihood for large phylogenies," Bioinformatics, vol. 28, no. 20, pp. 2689-2690, 2012. [Online]. Available: http://bioinformatics. oxfordjournals.org/content/28/20/2689.abstract
-
Bioinformatics
, vol.28
, Issue.20
, pp. 2689-2690
-
-
Smith, S.A.1
O'Meara, B.C.2
-
15
-
-
79955119965
-
A distance-based least-square method for dating speciation events
-
X. Xia and Q. Yang, "A distance-based least-square method for dating speciation events," Molecular Phylogenetics and Evolution, vol. 59, no. 2, pp. 342-353, 2011. [Online]. Available: http://www.sciencedirect.com/science/ article/pii/S1055790311000443
-
(2011)
Molecular Phylogenetics and Evolution
, vol.59
, Issue.2
, pp. 342-353
-
-
Xia, X.1
Yang, Q.2
-
16
-
-
84869752137
-
Estimating divergence times in large molecular phylogenies
-
K. Tamura, F. U. Battistuzzi, P. Billing-Ross, O. Murillo, A. Filipski, and S. Kumar, "Estimating divergence times in large molecular phylogenies," Proceedings of the National Academy of Sciences, 2012. [Online]. Available: http://www. pnas.org/content/early/2012/10/31/1213199109. abstract
-
(2012)
Proceedings of the National Academy of Sciences
-
-
Tamura, K.1
Battistuzzi, F.U.2
Billing-Ross, P.3
Murillo, O.4
Filipski, A.5
Kumar, S.6
-
17
-
-
0030749810
-
Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
-
Z. Yang and B. Rannala, "Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method," Molecular Biology and Evolution, vol. 14, pp. 717-724, 1997.
-
(1997)
Molecular Biology and Evolution
, vol.14
, pp. 717-724
-
-
Yang, Z.1
Rannala, B.2
-
18
-
-
0031741182
-
Estimating the rate of evolution of the rate of molecular evolution
-
J. Thorne, H. Kishino, and I. S. Painter, "Estimating the rate of evolution of the rate of molecular evolution," Molecular Biology and Evolution, vol. 15, pp. 1647-1657, 1998.
-
(1998)
Molecular Biology and Evolution
, vol.15
, pp. 1647-1657
-
-
Thorne, J.1
Kishino, H.2
Painter, I.S.3
-
19
-
-
0034077901
-
A compound Poisson process for relaxing the molecular clock
-
J. P. Huelsenbeck, B. Larget, and D. L. Swofford, "A compound Poisson process for relaxing the molecular clock," Genetics, vol. 154, pp. 1879-1892, 2000.
-
(2000)
Genetics
, vol.154
, pp. 1879-1892
-
-
Huelsenbeck, J.P.1
Larget, B.2
Swofford, D.L.3
-
20
-
-
0035103260
-
Performance of a divergence time estimation method under a probabilistic model of rate evolution
-
H. Kishino, J. L. Thorne, and W. Bruno, "Performance of a divergence time estimation method under a probabilistic model of rate evolution," Molecular Biology and Evolution, vol. 18, pp. 352-361, 2001.
-
(2001)
Molecular Biology and Evolution
, vol.18
, pp. 352-361
-
-
Kishino, H.1
Thorne, J.L.2
Bruno, W.3
-
21
-
-
0036803223
-
Divergence time and evolutionary rate estimation with multilocus data
-
J. Thorne and H. Kishino, "Divergence time and evolutionary rate estimation with multilocus data," Systematic Biology, vol. 51, pp. 689-702, 2002.
-
(2002)
Systematic Biology
, vol.51
, pp. 689-702
-
-
Thorne, J.1
Kishino, H.2
-
22
-
-
28944451210
-
Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
-
Z. Yang and B. Rannala, "Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds," Molecular Biology and Evolution, vol. 23, pp. 212-226, 2006.
-
(2006)
Molecular Biology and Evolution
, vol.23
, pp. 212-226
-
-
Yang, Z.1
Rannala, B.2
-
23
-
-
70350103638
-
Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times
-
S. Y. W. Ho and M. J. Phillips, "Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times," Systematic Biology, vol. 58, pp. 367-380, 2009.
-
(2009)
Systematic Biology
, vol.58
, pp. 367-380
-
-
Ho, S.Y.W.1
Phillips, M.J.2
-
24
-
-
82755190600
-
Temporally structured metapopulation dynamics and persistence of influenza a h3n2 virus in humans
-
J. Bahl, M. I. Nelson, K. H. Chan, R. Chen, D. Vijaykrishna, R. A. Halpin, T. B. Stockwell, X. Lin, D. E. Wentworth, E. Ghedin, Y. Guan, J. S. Malik Peiris, S. Riley, A. Rambaut, E. C. Holmes, and G. J. D. Smith, "Temporally structured metapopulation dynamics and persistence of influenza a h3n2 virus in humans," Proceedings of the National Academy of Sciences, 2011.
-
(2011)
Proceedings of the National Academy of Sciences
-
-
Bahl, J.1
Nelson, M.I.2
Chan, K.H.3
Chen, R.4
Vijaykrishna, D.5
Halpin, R.A.6
Stockwell, T.B.7
Lin, X.8
Wentworth, D.E.9
Ghedin, E.10
Guan, Y.11
Malik Peiris, J.S.12
Riley, S.13
Rambaut, A.14
Holmes, E.C.15
Smith, G.J.D.16
-
25
-
-
80855156756
-
Stepwise evolution of stable sociality in primates
-
S. Shultz, C. Opie, and Q. Atkinson, "Stepwise evolution of stable sociality in primates," Nature, vol. 479, no. 7372, pp. 219-222, 2011.
-
(2011)
Nature
, vol.479
, Issue.7372
, pp. 219-222
-
-
Shultz, S.1
Opie, C.2
Atkinson, Q.3
-
26
-
-
79961228770
-
The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi
-
D. Eastwood, D. Floudas, M. Binder, A. Majcherczyk, P. Schneider, A. Aerts, F. Asiegbu, S. Baker, K. Barry, M. Bendiksby et al., "The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi," Science, vol. 333, no. 6043, pp. 762-765, 2011.
-
(2011)
Science
, vol.333
, Issue.6043
, pp. 762-765
-
-
Eastwood, D.1
Floudas, D.2
Binder, M.3
Majcherczyk, A.4
Schneider, P.5
Aerts, A.6
Asiegbu, F.7
Baker, S.8
Barry, K.9
Bendiksby, M.10
-
27
-
-
84864346710
-
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
-
M. dos Reis, J. Inoue, M. Hasegawa, R. Asher, P. Donoghue, and Z. Yang, "Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny," Proceedings of the Royal Society B: Biological Sciences, vol. 279, no. 1742, pp. 3491-3500, 2012.
-
(2012)
Proceedings of the Royal Society B: Biological Sciences
, vol.279
, Issue.1742
, pp. 3491-3500
-
-
Dos Reis, M.1
Inoue, J.2
Hasegawa, M.3
Asher, R.4
Donoghue, P.5
Yang, Z.6
-
28
-
-
84859462115
-
Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K-T boundary in madagascar
-
A. Crottini, O. Madsen, C. Poux, A. Strauß, D. R. Vieites, and M. Vences, "Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the K-T boundary in madagascar," Proceedings of the National Academy of Sciences, vol. 109, no. 14, pp. 5358-5363, 2012.
-
(2012)
Proceedings of the National Academy of Sciences
, vol.109
, Issue.14
, pp. 5358-5363
-
-
Crottini, A.1
Madsen, O.2
Poux, C.3
Strauß, A.4
Vieites, D.R.5
Vences, M.6
-
29
-
-
34547803197
-
PAML 4: Phylogenetic Analysis by Maximum Likelihood
-
Z. Yang, "PAML 4: Phylogenetic Analysis by Maximum Likelihood," Molecular Biology and Evolution, vol. 24, no. 8, pp. 1586-1591, 2007. [Online]. Available: http://mbe.oxfordjournals.org/cgi/content/abstract/24/8/1586
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.8
, pp. 1586-1591
-
-
Yang, Z.1
-
30
-
-
69949126557
-
Phylobayes 3: A bayesian software package for phylogenetic reconstruction and molecular dating
-
N. Lartillot, T. Lepage, and S. Blanquart, "Phylobayes 3: a bayesian software package for phylogenetic reconstruction and molecular dating," Bioinformatics, vol. 25, no. 17, p. 2286, 2009.
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2286
-
-
Lartillot, N.1
Lepage, T.2
Blanquart, S.3
-
31
-
-
84864530626
-
Bayesian phylogenetics with beauti and the beast 1.7
-
A. J. Drummond, M. A. Suchard, D. Xie, and A. Rambaut, "Bayesian phylogenetics with beauti and the beast 1.7," Molecular Biology and Evolution, vol. 29, no. 8, pp. 1969-1973, 2012.
-
(2012)
Molecular Biology and Evolution
, vol.29
, Issue.8
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
32
-
-
77954967444
-
Bayesian estimation of divergence times from large sequence alignments
-
S. Guindon, "Bayesian estimation of divergence times from large sequence alignments," Molecular Biology and Evolu-tion, vol. 27, no. 8, pp. 1768-1781, 2010.
-
(2010)
Molecular Biology and Evolu-tion
, vol.27
, Issue.8
, pp. 1768-1781
-
-
Guindon, S.1
-
33
-
-
84860109324
-
Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space
-
F. Ronquist, M. Teslenko, P. van der Mark, D. L. Ayres, A. Darling, S. Höhna, B. Larget, L. Liu, M. A. Suchard, and J. P. Huelsenbeck, "Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space," Systematic Biology, vol. 61, no. 3, pp. 539-542, 2012.
-
(2012)
Systematic Biology
, vol.61
, Issue.3
, pp. 539-542
-
-
Ronquist, F.1
Teslenko, M.2
Mark Der P.Van3
Ayres, D.L.4
Darling, A.5
Höhna, S.6
Larget, B.7
Liu, L.8
Suchard, M.A.9
Huelsenbeck, J.P.10
-
34
-
-
79959462209
-
Approximate likelihood calculation on a phylogeny for bayesian estimation of divergence times
-
M. dos Reis and Z. Yang, "Approximate likelihood calculation on a phylogeny for bayesian estimation of divergence times," Molecular Biology and Evolution, vol. 28, no. 7, pp. 2161-2172, 2011.
-
(2011)
Molecular Biology and Evolution
, vol.28
, Issue.7
, pp. 2161-2172
-
-
Dos Reis, M.1
Yang, Z.2
-
35
-
-
84555188616
-
BEAGLE: An application programming interface and highperformance computing library for statistical phylogenetics
-
D. L. Ayers, A. Darling, D. J. Zwickl, P. Beerli, M. T. Holder, P. O. Lewis, J. P. Huelsenbeck, F. Ronquist, D. L. Swofford, M. P. Cummings, A. Rambaut, and M. A. Suchard, "BEAGLE: An application programming interface and highperformance computing library for statistical phylogenetics," Systematic Biology, vol. 61, pp. 170-173, 2012.
-
(2012)
Systematic Biology
, vol.61
, pp. 170-173
-
-
Ayers, D.L.1
Darling, A.2
Zwickl, D.J.3
Beerli, P.4
Holder, M.T.5
Lewis, P.O.6
Huelsenbeck, J.P.7
Ronquist, F.8
Swofford, D.L.9
Cummings, M.P.10
Rambaut, A.11
Suchard, M.A.12
-
36
-
-
84865146139
-
Raxml-light: A tool for computing terabyte phylogenies
-
A. Stamatakis, A. Aberer, C. Goll, S. Smith, S. Berger, and F. Izquierdo-Carrasco, "Raxml-light: a tool for computing terabyte phylogenies," Bioinformatics, vol. 28, no. 15, pp. 2064-2066, 2012.
-
(2012)
Bioinformatics
, vol.28
, Issue.15
, pp. 2064-2066
-
-
Stamatakis, A.1
Aberer, A.2
Goll, C.3
Smith, S.4
Berger, S.5
Izquierdo-Carrasco, F.6
-
38
-
-
84867418544
-
The multi-processor scheduling problem in phylogenetics
-
PhD Forum (IPDPSW) 2012 IEEE 26th International. IEEE
-
J. Zhang and A. Stamatakis, "The multi-processor scheduling problem in phylogenetics," in Parallel and Distributed Processing Symposium Workshops & PhD Forum (IPDPSW), 2012 IEEE 26th International. IEEE, 2012, pp. 691-698.
-
(2012)
Parallel and Distributed Processing Symposium Workshops
, pp. 691-698
-
-
Zhang, J.1
Stamatakis, A.2
-
39
-
-
83255165385
-
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees
-
F. Izquierdo-Carrasco, S. Smith, and A. Stamatakis, "Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees," BMC bioinformatics, vol. 12, no. 1, p. 470, 2011.
-
(2011)
BMC Bioinformatics
, vol.12
, Issue.1
, pp. 470
-
-
Izquierdo-Carrasco, F.1
Smith, S.2
Stamatakis, A.3
-
41
-
-
0019797407
-
Evolutionary trees from dna sequences: A maximum likelihood approach
-
J. Felsenstein, "Evolutionary trees from dna sequences: a maximum likelihood approach," Journal of molecular evo-lution, vol. 17, no. 6, pp. 368-376, 1981.
-
(1981)
Journal of Molecular Evo-lution
, vol.17
, Issue.6
, pp. 368-376
-
-
Felsenstein, J.1
-
42
-
-
84867419656
-
Orchestrating the phylogenetic likelihood function on emerging parallel architectures
-
B. Schmidt, Ed. CRC Press
-
A. Stamatakis, "Orchestrating the phylogenetic likelihood function on emerging parallel architectures," Bioinformatics-High Performance Parallel Computer Architectures, B. Schmidt, Ed. CRC Press, pp. 85-115, 2011.
-
(2011)
Bioinformatics-High Performance Parallel Computer Architectures
, pp. 85-115
-
-
Stamatakis, A.1
-
43
-
-
80055070300
-
Impacts of the cretaceous terrestrial revolution and kpg extinction on mammal diversification
-
R. W. Meredith, J. E. Jane?cka, J. Gatesy, O. A. Ryder, C. A. Fisher, E. C. Teeling, A. Goodbla, E. Eizirik, T. L. L. Simão, T. Stadler, D. L. Rabosky, R. L. Honeycutt, J. J. Flynn, C. M. Ingram, C. Steiner, T. L. Williams, T. J. Robinson, A. Burk-Herrick, M. Westerman, N. A. Ayoub, M. S. Springer, and W. J. Murphy, "Impacts of the cretaceous terrestrial revolution and kpg extinction on mammal diversification," Science, vol. 334, no. 6055, pp. 521-524, 2011.
-
(2011)
Science
, vol.334
, Issue.6055
, pp. 521-524
-
-
Meredith, R.W.1
-
44
-
-
1042304216
-
APE: Analyses of phylogenetics and evolution in R language
-
E. Paradis, J. Claude, and K. Strimmer, "APE: analyses of phylogenetics and evolution in R language," Bioinformatics, vol. 20, pp. 289-290, 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 289-290
-
-
Paradis, E.1
Claude, J.2
Strimmer, K.3
-
45
-
-
0030928378
-
Seq-gen: An application for the monte carlo simulation of dna sequence evolution along phylogenetic trees
-
A. Rambaut and N. Grass, "Seq-gen: an application for the monte carlo simulation of dna sequence evolution along phylogenetic trees," Comput Appl Biosci, vol. 13, no. 3, pp. 235-238, 1997.
-
(1997)
Comput Appl Biosci
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grass, N.2
-
46
-
-
57149096433
-
Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures
-
A. Stamatakis and M. Ott, "Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures," Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 363, no. 1512, pp. 3977-3984, 2008.
-
(2008)
Philosophical Transactions of the Royal Society B: Biological Sciences
, vol.363
, Issue.1512
, pp. 3977-3984
-
-
Stamatakis, A.1
Ott, M.2
|