-
1
-
-
16344379182
-
Covarion structure in plastid genome evolution: A new statistical test
-
DOI 10.1093/molbev/msi076
-
Ané C, Burleigh JG, McMahon MM, Sanderson MJ. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol Biol Evol. 22(4):914-924. (Pubitemid 40471405)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.4
, pp. 914-924
-
-
Ane, C.1
Burleigh, J.G.2
McMahon, M.M.3
Sanderson, M.J.4
-
2
-
-
33745584327
-
An improved statistical method for detecting heterotachy in nucleotide sequences
-
DOI 10.1093/molbev/msl006
-
Baele G, Raes J, Peer Y, Vansteelandt S. 2006. An improved statistical method for detecting heterotachy in nucleotide sequences. Mol Biol Evol. 23:1397-1405. (Pubitemid 43992340)
-
(2006)
Molecular Biology and Evolution
, vol.23
, Issue.7
, pp. 1397-1405
-
-
Baele, G.1
Raes, J.2
Van De Peer, Y.3
Vansteelandt, S.4
-
3
-
-
27744524191
-
An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics
-
DOI 10.1080/10635150500234609
-
Brinkmann H, Giezen M, Zhou Y, Raucourt GP, Philippe H. 2005. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol. 54(5):743-757. (Pubitemid 43142294)
-
(2005)
Systematic Biology
, vol.54
, Issue.5
, pp. 743-757
-
-
Brinkmann, H.1
Van Der Giezen, M.2
Zhou, Y.3
De Raucourt, G.P.4
Philippe, H.5
-
4
-
-
27844438226
-
Genome-scale evidence of the nematode-arthropod clade
-
Dopazo H, Dopazo J. 2005. Genome-scale evidence of the nematode-arthropod clade. Genome Biol. 6:R41.
-
(2005)
Genome Biol
, vol.6
-
-
Dopazo, H.1
Dopazo, J.2
-
5
-
-
0014860857
-
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
-
Fitch WM, Markowitz E. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet. 4:579-593.
-
(1970)
Biochem Genet
, vol.4
, pp. 579-593
-
-
Fitch, W.M.1
Markowitz, E.2
-
6
-
-
67749108209
-
INDELible: A flexible simulator of biological sequence evolution
-
Fletcher W, Yang Z. 2009. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol. 26(8):1879-1888.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.8
, pp. 1879-1888
-
-
Fletcher, W.1
Yang, Z.2
-
7
-
-
26444612274
-
Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous
-
DOI 10.1093/molbev/msi212
-
Gadagkar SR, Kumar S. 2005. Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol. 22:2139-2141. (Pubitemid 41437794)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.11
, pp. 2139-2141
-
-
Gadagkar, S.R.1
Kumar, S.2
-
8
-
-
0035029534
-
Maximum-likelihood phylogenetic analysis under a covarion-like model
-
Galtier N. 2001. Maximum-likelihood phylogenetic analysis under a covarion-like model. Mol Biol Evol. 18:866-873. (Pubitemid 32372956)
-
(2001)
Molecular Biology and Evolution
, vol.18
, Issue.5
, pp. 866-873
-
-
Galtier, N.1
-
9
-
-
45849119373
-
Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites
-
DOI 10.1093/molbev/msn098
-
Gruenheit N, Lockhart PJ, Steel M, Martin W. 2008. Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites. Mol Biol Evol. 25:1512-1520. (Pubitemid 351882028)
-
(2008)
Molecular Biology and Evolution
, vol.25
, Issue.7
, pp. 1512-1520
-
-
Gruenheit, N.1
Lockhart, P.J.2
Steel, M.3
Martin, W.4
-
10
-
-
0036097894
-
Testing a covariotide model of DNA substitution
-
Huelsenbeck JP. 2002. Testing a covariotide model of DNA substitution. Mol Biol Evol. 19:698-707. (Pubitemid 34521301)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.5
, pp. 698-707
-
-
Huelsenbeck, J.P.1
-
11
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogenous
-
DOI 10.1038/nature02917
-
Kolaczkowski B, Thornton JW. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980-984. (Pubitemid 39434418)
-
(2004)
Nature
, vol.431
, Issue.7011
, pp. 980-984
-
-
Kolaczkowski, B.1
Thomton, J.W.2
-
12
-
-
44649184070
-
A mixed branch length model of heterotachy improves phylogenetic accuracy
-
Kolaczkowski B, Thornton JW. 2008. A mixed branch length model of heterotachy improves phylogenetic accuracy. Mol Biol Evol. 25:1054-1066.
-
(2008)
Mol Biol Evol
, vol.25
, pp. 1054-1066
-
-
Kolaczkowski, B.1
Thornton, J.W.2
-
13
-
-
28944440718
-
Heterotachy and tree building: A case study with plastids and eu-bacteria
-
Lockhart PJ, Novis P, Milligan BG, Riden J, Rambaut A, Larkumk T. 2005. Heterotachy and tree building: a case study with plastids and eu-bacteria. Mol Biol Evol. 23:40-45.
-
(2005)
Mol Biol Evol
, vol.23
, pp. 40-45
-
-
Lockhart, P.J.1
Novis, P.2
Milligan, B.G.3
Riden, J.4
Rambaut, A.5
Larkumk, T.6
-
14
-
-
0031852105
-
A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages
-
Lockhart PJ, Steel MA, Barbrook AC, Huson DH, Charleston MA, Howe CJ. 1998. A covariotide model explains apparent phyloge-netic structure of oxygenic photosynthetic lineages. Mol Biol Evol. 15:1183-1188. (Pubitemid 28394953)
-
(1998)
Molecular Biology and Evolution
, vol.15
, Issue.9
, pp. 1183-1188
-
-
Lockhart, P.J.1
Steel, M.A.2
Barbrook, A.C.3
Huson, D.H.4
Charleston, M.A.5
Howe, C.J.6
-
15
-
-
0036134757
-
Heterotachy, an important process of protein evolution
-
Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol. 19(1):1-7. (Pubitemid 34008041)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.1
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
16
-
-
0032825223
-
The root of the tree of life in the light of the covarion model
-
DOI 10.1007/PL00006572
-
Lopez P, Forterre P, Philippe H. 1999. The root of the tree of life in light of the covarion model. J Mol Evol. 49:496-508. (Pubitemid 29463392)
-
(1999)
Journal of Molecular Evolution
, vol.49
, Issue.4
, pp. 496-508
-
-
Lopez, P.1
Forterre, P.2
Philippe, H.3
-
17
-
-
0036789261
-
An empirical analysis of mt 16S rRNA covarion-like evolution in insects: Site-specific rate variation is clustered and frequently detected
-
Misof B, Anderson CL, Buckley TR, Erpenbeck D, Rickert A, Misof K. 2002. An empirical analysis of mt 16S rRNA covarion-like evolution in insects: site-specific rate variation is clustered and frequently detected. J Mol Evol. 55:460-469.
-
(2002)
J Mol Evol
, vol.55
, pp. 460-469
-
-
Misof, B.1
Anderson, C.L.2
Buckley, T.R.3
Erpenbeck, D.4
Rickert, A.5
Misof, K.6
-
18
-
-
39749188544
-
Rooting the eutherian tree: The power and pitfalls of phylogenomics
-
Nishihara H, Okada N, Hasegawa M. 2007. Rooting the eutherian tree: the power and pitfalls of phylogenomics. Genome Biol. 8(9): R199.
-
(2007)
Genome Biol
, vol.8
, Issue.9
-
-
Nishihara, H.1
Okada, N.2
Hasegawa, M.3
-
19
-
-
17744386162
-
Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and protostomia
-
DOI 10.1093/molbev/msi111
-
Philippe H, Lartillot N, Brinkmann H. 2005. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdyso-zoa, Lophotrochozoa, and Protostomia. Mol Biol Evol. 22:1246-1253. (Pubitemid 40577762)
-
(2005)
Molecular Biology and Evolution
, vol.22
, Issue.5
, pp. 1246-1253
-
-
Philippe, H.1
Lartillot, N.2
Brinkmann, H.3
-
20
-
-
27744488568
-
Het-erotachy and long-branch attraction in phylogenetics
-
Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F. 2005. Het-erotachy and long-branch attraction in phylogenetics. Evol Biol. 5(1):50.
-
(2005)
Evol Biol
, vol.5
, Issue.1
, pp. 50
-
-
Philippe, H.1
Zhou, Y.2
Brinkmann, H.3
Rodrigue, N.4
Delsuc, F.5
-
21
-
-
0035527410
-
A comparison of different strategies for selecting models of DNA substitution
-
Posada D, Crandall KA. 2001. A comparison of different strategies for selecting models of DNA substitution. Syst Biol. 50:580-601.
-
(2001)
Syst Biol
, vol.50
, pp. 580-601
-
-
Posada, D.1
Crandall, K.A.2
-
22
-
-
0030928378
-
Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238. (Pubitemid 27249927)
-
(1997)
Computer Applications in the Biosciences
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
23
-
-
38849160068
-
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
-
DOI 10.1101/gr.7105007
-
Rasmussen MD, Kellis M. 2007. Accurate gene-tree reconstruction by learning gene-and species-specific substitution rates across multiple complete genomes. Genome Res. 17:1932-1942. (Pubitemid 351369026)
-
(2007)
Genome Research
, vol.17
, Issue.12
, pp. 1932-1942
-
-
Rasmussen, M.D.1
Kellis, M.2
-
24
-
-
33847637949
-
Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta
-
DOI 10.1093/molbev/msl200
-
Rodriguez-Ezpeleta N, Philippe H, Brinkmann H, Becker B, Melkonian M. 2007. Phylogenetic analyses of nuclear, mito-chondrial, and plastid multigene data sets support the placement of mesostigma in the streptophyta. Mol Biol Evol. 24(3):723-731. (Pubitemid 46355796)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.3
, pp. 723-731
-
-
Rodriguez-Ezpeleta, N.1
Philippe, H.2
Brinkmann, H.3
Becker, B.4
Melkonian, M.5
-
25
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing evolutionary trees
-
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing evolutionary trees. Mol Biol Evol. 4: 406-425.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
26
-
-
84907319426
-
Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions
-
Self SG, Liang KY. 1987. Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions. J Amer Statist Assoc. 82:605-610.
-
(1987)
J Amer Statist Assoc
, vol.82
, pp. 605-610
-
-
Self, S.G.1
Liang, K.Y.2
-
27
-
-
0024661142
-
Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated
-
Shoemaker JS, Fitch WM. 1989. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol Biol Evol. 6:270-289.
-
(1989)
Mol Biol Evol
, vol.6
, pp. 270-289
-
-
Shoemaker, J.S.1
Fitch, W.M.2
-
28
-
-
67649649922
-
The effect of heterotachy in multigene analysis using the neighbor joining method
-
Som A, Fuellen G. 2009. The effect of heterotachy in multigene analysis using the neighbor joining method. Mol Phylogenet Evol. 52(3):846-851.
-
(2009)
Mol Phylogenet Evol
, vol.52
, Issue.3
, pp. 846-851
-
-
Som, A.1
Fuellen, G.2
-
29
-
-
17744400517
-
Likelihood, parsimony and heterogeneous evolution
-
Spencer M, Susko E, Roger AJ. 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
-
30
-
-
0242487523
-
Estimation of Rates-Across-Sites Distributions in Phylogenetic Substitution Models
-
DOI 10.1080/10635150390235395
-
Susko E, Field C, Blouin C, Roger AJ. 2003. Estimation of rates-across-sites distributions in phylogenetic substitution models. Syst Biol. 52:594-603. (Pubitemid 37365042)
-
(2003)
Systematic Biology
, vol.52
, Issue.5
, pp. 594-603
-
-
Susko, E.1
Field, C.2
Blouin, C.3
Roger, A.J.4
-
31
-
-
0036730253
-
Testing for differences in rates-across-sites distributions in phylogenetic subtrees
-
Susko E, InagakiY, FieldC, Holder ME, Roger AJ. 2002. Testing for differences in rates-across-sites distributions in phylogenetic subtrees. Mol Biol Evol. 19(9):1514-1523. (Pubitemid 36752776)
-
(2002)
Molecular Biology and Evolution
, vol.19
, Issue.9
, pp. 1514-1523
-
-
Susko, E.1
Inagaki, Y.2
Field, C.3
Holder, M.E.4
Roger, A.J.5
-
32
-
-
35748943561
-
On reduced amino acid alphabets for phylo-genetic inference
-
Susko E, Roger AJ. 2007. On reduced amino acid alphabets for phylo-genetic inference. Mol Biol Evol. 24:2139-2150.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 2139-2150
-
-
Susko, E.1
Roger, A.J.2
-
33
-
-
0031986279
-
Modeling the covarion hypothesis of nucleotide substitution
-
PII S0025556497000813
-
Tuffley C, Steel MA. 1998. Modelling the covarion hypothesis of nu-cleotide substitution. Math Biosci. 147:63-91. (Pubitemid 128761931)
-
(1998)
Mathematical Biosciences
, vol.147
, Issue.1
, pp. 63-91
-
-
Tuffley, C.1
Steel, M.2
-
34
-
-
33845900956
-
Testing for covarion-like evolution in protein sequences
-
DOI 10.1093/molbev/msl155
-
Wang H, Spencer M, Susko E, Roger AJ. 2007. Testing for covarion-like evolution in protein sequences. Mol Biol Evol. 24:294-305. (Pubitemid 46026302)
-
(2007)
Molecular Biology and Evolution
, vol.24
, Issue.1
, pp. 294-305
-
-
Wang, H.-C.1
Spencer, M.2
Susko, E.3
Roger, A.J.4
-
36
-
-
70549113148
-
General heterotachy and distance method adjustments
-
Wu J, Susko E. 2009. General heterotachy and distance method adjustments. Mol Biol Evol. 26:2689-2697.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 2689-2697
-
-
Wu, J.1
Susko, E.2
-
37
-
-
77649340046
-
Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons
-
Wu J, Susko E. 2010. Rate-variation need not defeat phylogenetic inference through pairwise sequence comparisons. J Theor Biol. 263(4):587-589.
-
(2010)
J Theor Biol
, vol.263
, Issue.4
, pp. 587-589
-
-
Wu, J.1
Susko, E.2
-
38
-
-
38949188205
-
An independent heterotachy model and its implications for phylogeny and divergence time estimation
-
Wu J, Susko E, Roger AJ. 2007. An independent heterotachy model and its implications for phylogeny and divergence time estimation. Mol Phyl Evol. 46:801-806.
-
(2007)
Mol Phyl Evol
, vol.46
, pp. 801-806
-
-
Wu, J.1
Susko, E.2
Roger, A.J.3
-
39
-
-
0027132974
-
Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
-
Yang Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396-1401. (Pubitemid 23352619)
-
(1993)
Molecular Biology and Evolution
, vol.10
, Issue.6
, pp. 1396-1401
-
-
Yang, Z.1
-
40
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
-
Yang Z. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol. 39:306-314. (Pubitemid 24283346)
-
(1994)
Journal of Molecular Evolution
, vol.39
, Issue.3
, pp. 306-314
-
-
Yang, Z.1
-
41
-
-
74549146721
-
A Dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests
-
Zhou Y, Brinkmann H, Rodrigue N, Philippe H. 2010. A Dirichlet process covarion mixture model and its assessments using posterior predictive discrepancy tests. Mol Biol Evol. 27:371-384.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 371-384
-
-
Zhou, Y.1
Brinkmann, H.2
Rodrigue, N.3
Philippe, H.4
|