-
1
-
-
16344379182
-
Covarion structure in plastid genome evolution: A new statistical test
-
Ane, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in plastid genome evolution: A new statistical test. Mol. Biol. Evol. 22:914-924.
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 914-924
-
-
Ane, C.1
Burleigh, J.G.2
McMahon, M.M.3
Sanderson, M.J.4
-
2
-
-
21244454414
-
Substantial regional variation in substitution rates in the human genome: Importance of GC content, gene density, and telomere-specific effects
-
Arndt, P. F., T. Hwa, and D. A. Petrov. 2005. Substantial regional variation in substitution rates in the human genome: Importance of GC content, gene density, and telomere-specific effects. J. Mol. Evol. 60:748-763.
-
(2005)
J. Mol. Evol
, vol.60
, pp. 748-763
-
-
Arndt, P.F.1
Hwa, T.2
Petrov, D.A.3
-
3
-
-
33847243366
-
Assessing among-locus variation in the inference of seed plant phylogeny
-
Burleigh, J. G., and S. Mathews. 2007. Assessing among-locus variation in the inference of seed plant phylogeny. Int. J. Plant Sci. 168:111-124.
-
(2007)
Int. J. Plant Sci
, vol.168
, pp. 111-124
-
-
Burleigh, J.G.1
Mathews, S.2
-
5
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
6
-
-
85142197241
-
-
Fujisawa, H., S. Eguchi, M. Ushijima, S. Miyata, Y. Miki, T. Muto, and M. Matsuura. 2004. Genotyping of single nucleotide polymorphism using model-based clustering. Bioinformatics 20:718-U489.
-
Fujisawa, H., S. Eguchi, M. Ushijima, S. Miyata, Y. Miki, T. Muto, and M. Matsuura. 2004. Genotyping of single nucleotide polymorphism using model-based clustering. Bioinformatics 20:718-U489.
-
-
-
-
7
-
-
26444612274
-
Maximum-likelihood outperforms maximum-parsimony even when evolutionary rates are heterotachous
-
Gadagkar, S. R., and S. Kumar. 2005. Maximum-likelihood outperforms maximum-parsimony even when evolutionary rates are heterotachous. Mol. Biol. Evol. 22:2139-2141.
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 2139-2141
-
-
Gadagkar, S.R.1
Kumar, S.2
-
8
-
-
26444556992
-
A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous
-
Gaucher, E. A., and M. M. Miyamoto. 2005. A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous. Mol. Phyl. Evol. 37:928-931.
-
(2005)
Mol. Phyl. Evol
, vol.37
, pp. 928-931
-
-
Gaucher, E.A.1
Miyamoto, M.M.2
-
9
-
-
0004012196
-
-
2nd edition. Chapman & Hall/CRC, New York
-
Gelman, A., J. B. Carlin, H. S. Stern, and D. B. Rubin. 2003. Bayesian data analysis, 2nd edition. Chapman & Hall/CRC, New York.
-
(2003)
Bayesian data analysis
-
-
Gelman, A.1
Carlin, J.B.2
Stern, H.S.3
Rubin, D.B.4
-
10
-
-
0035649909
-
A penalized likelihood approach to image warping
-
Glasbey, C. A., and K. V. Mardia. 2001. A penalized likelihood approach to image warping. J. R. Stat. Soc. B 63:465-492.
-
(2001)
J. R. Stat. Soc. B
, vol.63
, pp. 465-492
-
-
Glasbey, C.A.1
Mardia, K.V.2
-
11
-
-
0038048942
-
Parsimony, likelihood, and simplicity
-
Goloboff, P. A. 2003. Parsimony, likelihood, and simplicity. Cladistics 19:91-103.
-
(2003)
Cladistics
, vol.19
, pp. 91-103
-
-
Goloboff, P.A.1
-
12
-
-
0003684449
-
-
Springer, New York
-
Hastie, T., R. Tibshirani, and J. H. Friedman. 2001. The elements of statistical learning: Data mining, inference, and prediction. Springer, New York.
-
(2001)
The elements of statistical learning: Data mining, inference, and prediction
-
-
Hastie, T.1
Tibshirani, R.2
Friedman, J.H.3
-
13
-
-
45849120228
-
A Bayesian perspective on a non-parsimonious parsimony model
-
Huelsenbeck, J. P., C. Ané, B. Larget, and F. Ronquist. 2008. A Bayesian perspective on a non-parsimonious parsimony model. Syst. Biol. 57:406-419.
-
(2008)
Syst. Biol
, vol.57
, pp. 406-419
-
-
Huelsenbeck, J.P.1
Ané, C.2
Larget, B.3
Ronquist, F.4
-
14
-
-
2442671519
-
Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
-
Huelsenbeck, J. P., B. Larget, and M. Alfaro. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123-1133.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1123-1133
-
-
Huelsenbeck, J.P.1
Larget, B.2
Alfaro, M.3
-
15
-
-
33645850710
-
Phylogenomics: The beginning of incongruence?
-
Jeffroy, O., H. Brinkmann, F. Delsuc, and H. Philippe. 2006. Phylogenomics: The beginning of incongruence? Trends Genet. 22:225-231.
-
(2006)
Trends Genet
, vol.22
, pp. 225-231
-
-
Jeffroy, O.1
Brinkmann, H.2
Delsuc, F.3
Philippe, H.4
-
16
-
-
33846675265
-
A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group
-
Kawahara, Y., and T. Imanishi. 2007. A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group. BMC Evol. Biol. 7.
-
(2007)
BMC Evol. Biol
, vol.7
-
-
Kawahara, Y.1
Imanishi, T.2
-
17
-
-
0035881655
-
Macroevolution of the hairy enhancer in Drosophila species
-
Kim, J. 2001. Macroevolution of the hairy enhancer in Drosophila species. J. Exp. Zool. (Mol. Dev. Evol.) 291:175-185.
-
(2001)
J. Exp. Zool. (Mol. Dev. Evol.)
, vol.291
, pp. 175-185
-
-
Kim, J.1
-
18
-
-
7244221755
-
Performance of maximum-parsimony and likelihood phylogenetics when evolution is heterogeneous
-
Kolaczkowski, B., and J. W. Thornton. 2004. Performance of maximum-parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984.
-
(2004)
Nature
, vol.431
, pp. 980-984
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
19
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
Lartillot, N., and H. Philippe 2004. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21:1095-1109.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
20
-
-
19044373497
-
Polytomies and Bayesian phylogenetic inference
-
Lewis, P. O., M. T. Holder, and K. E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54:241-253.
-
(2005)
Syst. Biol
, vol.54
, pp. 241-253
-
-
Lewis, P.O.1
Holder, M.T.2
Holsinger, K.E.3
-
21
-
-
0003421005
-
-
Sinauer, Sunderland, Massachusetts
-
Li, W.-H. 1997. Molecular evolution. Sinauer, Sunderland, Massachusetts.
-
(1997)
Molecular evolution
-
-
Li, W.-H.1
-
22
-
-
26444605036
-
A tale of two processes
-
Lockhart, P., and M. Steel. 2005. A tale of two processes. Syst. Biol. 54:948-951.
-
(2005)
Syst. Biol
, vol.54
, pp. 948-951
-
-
Lockhart, P.1
Steel, M.2
-
23
-
-
25844516325
-
Phylogenetic MCMC algorithms are misleading on mixtures of trees
-
Mossel, E., and E. Vigoda. 2005. Phylogenetic MCMC algorithms are misleading on mixtures of trees. Science 309:2207-2209.
-
(2005)
Science
, vol.309
, pp. 2207-2209
-
-
Mossel, E.1
Vigoda, E.2
-
24
-
-
0034538773
-
A survey of truncated-Newton methods
-
Nash, S. G. 2000. A survey of truncated-Newton methods. J. Comput. Appl. Math. 124:45-59.
-
(2000)
J. Comput. Appl. Math
, vol.124
, pp. 45-59
-
-
Nash, S.G.1
-
26
-
-
53849121558
-
-
Nguyen, X. L. and M. I. Jordan. 2003. On the concentration of expectation and approximate inference in layered networks. Adv. Neural. Inform. Proc. Syst. (NIPS) 17. MIT Press, Cambridge, Massachusetts.
-
Nguyen, X. L. and M. I. Jordan. 2003. On the concentration of expectation and approximate inference in layered networks. Adv. Neural. Inform. Proc. Syst. (NIPS) 17. MIT Press, Cambridge, Massachusetts.
-
-
-
-
27
-
-
0027957393
-
fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum-likelihood
-
Olsen, G. J., H. Matsuda, R. Hagstrom, and R. Overbeek. 1994. fastDNAml: A tool for construction of phylogenetic trees of DNA sequences using maximum-likelihood. Comput. Appl. Biosci. 10:41-48.
-
(1994)
Comput. Appl. Biosci
, vol.10
, pp. 41-48
-
-
Olsen, G.J.1
Matsuda, H.2
Hagstrom, R.3
Overbeek, R.4
-
28
-
-
4243140058
-
A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
-
Pagel, M., and A. Meade. 2004. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst. Biol. 53:571-581.
-
(2004)
Syst. Biol
, vol.53
, pp. 571-581
-
-
Pagel, M.1
Meade, A.2
-
29
-
-
34548550647
-
Alternative penalty functions for penalized likelihood principal components
-
Park, T. 2007. Alternative penalty functions for penalized likelihood principal components. J. Appl. Stat. 34:767-777.
-
(2007)
J. Appl. Stat
, vol.34
, pp. 767-777
-
-
Park, T.1
-
30
-
-
27744441025
-
-
Philippe, H., F. Delsuc, H. Brinkmann, and N. Lartillot. 2005. Phylogenomics. Ann. Rev. Ecol. Evol. Syst. 36:541-562.
-
(2005)
Phylogenomics. Ann. Rev. Ecol. Evol. Syst
, vol.36
, pp. 541-562
-
-
Philippe, H.1
Delsuc, F.2
Brinkmann, H.3
Lartillot, N.4
-
31
-
-
53849118748
-
Fast variational inference for large-scale internet diagnosis. Neural Inform
-
Platt, J. C., E. Kiciman and D. A. Maltz. 2008. Fast variational inference for large-scale internet diagnosis. Neural Inform. Proc. Syst., 2007, vol. 20.
-
(2007)
Proc. Syst
, vol.20
-
-
Platt, J.C.1
Kiciman, E.2
Maltz, D.A.3
-
32
-
-
0000215283
-
Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris Zone
-
Siddall, M. E. 1998. Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris Zone. Cladistics 14:209-220.
-
(1998)
Cladistics
, vol.14
, pp. 209-220
-
-
Siddall, M.E.1
-
33
-
-
33645106224
-
The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters
-
Simmons, M. P., L. B. Zhang, C. T. Webb, A. Reeves, and J. A. Miller. 2006. The relative performance of Bayesian and parsimony approaches when sampling characters evolving under homogeneous and heterogeneous sets of parameters. Cladistics 22:171-185.
-
(2006)
Cladistics
, vol.22
, pp. 171-185
-
-
Simmons, M.P.1
Zhang, L.B.2
Webb, C.T.3
Reeves, A.4
Miller, J.A.5
-
34
-
-
15544387147
-
Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster
-
Singh, N. D., P. F. Arndt, and D. A. Petrov. 2005. Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster. Genetics 169:709-722.
-
(2005)
Genetics
, vol.169
, pp. 709-722
-
-
Singh, N.D.1
Arndt, P.F.2
Petrov, D.A.3
-
35
-
-
0004290632
-
-
MIT Press, Cambridge, Massachusetts
-
Sober, E. 1988. Reconstructing the past. MIT Press, Cambridge, Massachusetts.
-
(1988)
Reconstructing the past
-
-
Sober, E.1
-
36
-
-
17744400517
-
Likelihood, parsimony, and heterogeneous evolution
-
Spencer, M., E. Susko, and A. J. Roger. 2005. Likelihood, parsimony, and heterogeneous evolution. Mol. Biol. Evol. 22:1161-1164.
-
(2005)
Mol. Biol. Evol
, vol.22
, pp. 1161-1164
-
-
Spencer, M.1
Susko, E.2
Roger, A.J.3
-
37
-
-
33750403801
-
RAxML-VI-HPC: Maximum-likelihood-based phylogenetic analyses with thousands of taxa and mixed models
-
Stamatakis, A. 2006. RAxML-VI-HPC: Maximum-likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
-
(2006)
Bioinformatics
, vol.22
, pp. 2688-2690
-
-
Stamatakis, A.1
-
38
-
-
2242465833
-
Sufficient conditions for two tree reconstruction techniques to succeed on sufficiently long sequences
-
Steel, M. 2001. Sufficient conditions for two tree reconstruction techniques to succeed on sufficiently long sequences. SIAM J. Disc. Math. 14:36-48.
-
(2001)
SIAM J. Disc. Math
, vol.14
, pp. 36-48
-
-
Steel, M.1
-
40
-
-
3042545431
-
On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled
-
Susko, E., Y. Inagaki, and A. J. Roger. 2004. On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Mol. Biol. Evol. 21:1629-1642.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1629-1642
-
-
Susko, E.1
Inagaki, Y.2
Roger, A.J.3
-
41
-
-
0001336205
-
Phylogenetic inference
-
D. M. Hillis, C. Moritz, and B. K. Mable, eds, Sinauer, Sunderland, Massachusetts
-
Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
-
(1996)
Molecular systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
42
-
-
0141706951
-
The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi
-
Tehler, A., D. P. Little, and J. S. Farris. 2003. The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi. Fungi Mycol. Res. 107:901-916.
-
(2003)
Fungi Mycol. Res
, vol.107
, pp. 901-916
-
-
Tehler, A.1
Little, D.P.2
Farris, J.S.3
-
43
-
-
34347383963
-
Protein evolution constraints and model-based techniques to study them
-
Thorne, J. L. 2007. Protein evolution constraints and model-based techniques to study them. Curr. Opin. Struct. Biol. 17:337-341.
-
(2007)
Curr. Opin. Struct. Biol
, vol.17
, pp. 337-341
-
-
Thorne, J.L.1
-
44
-
-
0031149251
-
Links between maximum-likelihood and maximum-parsimony under a simple model of site substitution
-
Tuffley, C., and M. Steel. 1997. Links between maximum-likelihood and maximum-parsimony under a simple model of site substitution. Bull. Math. Biol. 59:581-607.
-
(1997)
Bull. Math. Biol
, vol.59
, pp. 581-607
-
-
Tuffley, C.1
Steel, M.2
-
45
-
-
0015219691
-
Fitting discrete probability distributions to evolutionary events
-
Uzzell, T., and K. W. Corbin. 1971. Fitting discrete probability distributions to evolutionary events. Science 172:1089-1096.
-
(1971)
Science
, vol.172
, pp. 1089-1096
-
-
Uzzell, T.1
Corbin, K.W.2
-
46
-
-
34347336584
-
Localizing recent adaptive evolution in the human genome
-
Williamson, S. H., M. J. Hubisz, A. G. Clark, B. A. Payseur, C. D. Bustamante, and R. Nielsen. 2007. Localizing recent adaptive evolution in the human genome. Plos Genet. 3:901-915.
-
(2007)
Plos Genet
, vol.3
, pp. 901-915
-
-
Williamson, S.H.1
Hubisz, M.J.2
Clark, A.G.3
Payseur, B.A.4
Bustamante, C.D.5
Nielsen, R.6
-
47
-
-
22844452772
-
Branch-length prior influences Bayesian posterior probability of phylogeny
-
Yang, Z., and B. Rannala. 2005. Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol. 54:455-470.
-
(2005)
Syst. Biol
, vol.54
, pp. 455-470
-
-
Yang, Z.1
Rannala, B.2
|