-
1
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H (1974) A new look at the statistical model identification. IEEE Trans Autom Control 19:716-723
-
(1974)
IEEE Trans Autom Control
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
2
-
-
16344379182
-
Covarion structure in plastid genome evolution: A new statistical test
-
Ane C, Burleigh JG, McMahon MM, Sanderson MJ (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
-
3
-
-
0034759844
-
Phylogeny of the Chlorophyceae with special reference to the Sphaeropleales: A study of 18S and 26S rDNA data
-
Buchheim MA, Michalopulos EA, Buchheim JA (2001) Phylogeny of the Chlorophyceae with special reference to the Sphaeropleales: A study of 18S and 26S rDNA data. Journal of Phycology, 37:819-835
-
(2001)
Journal of Phycology
, vol.37
, pp. 819-835
-
-
Buchheim, M.A.1
Michalopulos, E.A.2
Buchheim, J.A.3
-
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
-
-
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
-
(2001)
Mol Biol Evol
, vol.18
, pp. 866-873
-
-
Galtier, N.1
-
8
-
-
84972511893
-
Practical Markov chain Monte Carlo
-
Geyer CJ (1992) Practical Markov chain Monte Carlo. Stat Sci 7:473-483
-
(1992)
Stat Sci
, vol.7
, pp. 473-483
-
-
Geyer, C.J.1
-
9
-
-
0032923454
-
Variation in the pattern of nucleotide substitution across sites
-
Huelsenbeck JP (1999) Variation in the pattern of nucleotide substitution across sites. J Mol Evol 48:86-93
-
(1999)
J Mol Evol
, vol.48
, pp. 86-93
-
-
Huelsenbeck, J.P.1
-
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
-
(2002)
Mol Biol Evol
, vol.19
, pp. 698-707
-
-
Huelsenbeck, J.P.1
-
11
-
-
2942669900
-
Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss
-
Kiontke K, Gavin NP, Raynes Y, Roehrig C, Piano F, Fitch DHA (2004) Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proceedings of the National Academy of Sciences of the United States of America, 101:9003-9008
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, pp. 9003-9008
-
-
Kiontke, K.1
Gavin, N.P.2
Raynes, Y.3
Roehrig, C.4
Piano, F.5
Fitch, D.H.A.6
-
12
-
-
7244221755
-
Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous
-
Kolaczkowski B, Thornton J (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.2
-
13
-
-
0032529584
-
Models of natural mutations including site heterogeneity
-
Koshi JM, Goldstein RA (1998) Models of natural mutations including site heterogeneity. Proteins Struct Funct Genet 32:289-295
-
(1998)
Proteins Struct Funct Genet
, vol.32
, pp. 289-295
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
14
-
-
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 19:1-7
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1-7
-
-
Lopez, P.1
Casane, D.2
Philippe, H.3
-
15
-
-
4644320044
-
Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes
-
Mueller RL, Macey JR, Jaekel M, Wake DB, Boore JL (2004) Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proceedings of the National Academy of Sciences of the United States of America, 101:13820-13825
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, pp. 13820-13825
-
-
Mueller, R.L.1
Macey, J.R.2
Jaekel, M.3
Wake, D.B.4
Boore, J.L.5
-
16
-
-
4243140058
-
A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
-
Pagel M, Meade A (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
-
17
-
-
33644608263
-
Mixture models in phylogenetic inference
-
Gascuel O ed, Clarendon, Oxford
-
Pagel M, Meade A (2005) Mixture models in phylogenetic inference. In: Gascuel O (ed) Mathematics of evolution and phylogeny. Clarendon, Oxford, pp 121-142
-
(2005)
Mathematics of Evolution and Phylogeny
, pp. 121-142
-
-
Pagel, M.1
Meade, A.2
-
18
-
-
27744488568
-
Heterotachy and long-branch attraction in phylogenetics
-
Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F (2005) Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol 5:50
-
(2005)
BMC Evol Biol
, vol.5
, pp. 50
-
-
Philippe, H.1
Zhou, Y.2
Brinkmann, H.3
Rodrigue, N.4
Delsuc, F.5
-
19
-
-
0037556430
-
TreeBASE: A database of phylogenetic knowledge
-
J. Shimura, K. Wilson, and D. Gordon, eds, Tsukuba, Japan
-
Piel WH, Donoghue MJ, Sanderson MJ (2002) TreeBASE: a database of phylogenetic knowledge. pp 41-47 in: J. Shimura, K. Wilson, and D. Gordon, eds. The interoperable "Catalog of Life." Research Report, National Institute for Environmental Studies No. 171, Tsukuba, Japan
-
(2002)
The Interoperable "Catalog of Life." Research Report, National Institute for Environmental Studies No. 171
, pp. 41-47
-
-
Piel, W.H.1
Donoghue, M.J.2
Sanderson, M.J.3
-
20
-
-
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 235-238
-
(1997)
Comput Appl Biosci
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
21
-
-
0242365676
-
Genome-scale approaches to resolving incongruence in molecular phylogenies
-
Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804
-
(2003)
Nature
, vol.425
, pp. 798-804
-
-
Rokas, A.1
Williams, B.L.2
King, N.3
Carroll, S.B.4
-
22
-
-
0036177790
-
Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: Conflicting data, rooting problems, and the monophyly of conifers
-
Rydin C, Kallersjo M, Friist EM (2002) Seed plant relationships and the systematic position of Gnetales based on nuclear and chloroplast DNA: Conflicting data, rooting problems, and the monophyly of conifers. International Journal of Plant Sciences, 163:197-214
-
(2002)
International Journal of Plant Sciences
, vol.163
, pp. 197-214
-
-
Rydin, C.1
Kallersjo, M.2
Friist, E.M.3
-
23
-
-
33748041084
-
Heterotachy processes in rhodophyte-derived secondhand plastid genes: Implications for addressing the origin and evolution of dinoflagellate plastids
-
Shalchian-Tabrizi K, Skanseng M, Ronquist F, Klaveness D, Bachvaroff TR, Delwiche CF, Botnen A, Tengs T, Jakobsen KS (2006) Heterotachy processes in rhodophyte-derived secondhand plastid genes: implications for addressing the origin and evolution of dinoflagellate plastids. Mol Biol Evol 23:1504-1515
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1504-1515
-
-
Shalchian-Tabrizi, K.1
Skanseng, M.2
Ronquist, F.3
Klaveness, D.4
Bachvaroff, T.R.5
Delwiche, C.F.6
Botnen, A.7
Tengs, T.8
Jakobsen, K.S.9
-
24
-
-
33645223085
-
Systematics and evolution of the tropical monocot family Costaceae (Zingiberales): A multiple dataset approach
-
Specht CD (2006) Systematics and evolution of the tropical monocot family Costaceae (Zingiberales): A multiple dataset approach. Systematic Botany, 31:89-106
-
(2006)
Systematic Botany
, vol.31
, pp. 89-106
-
-
Specht, C.D.1
-
25
-
-
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
-
26
-
-
84900062551
-
-
Swofford DL, Olsen GJ, Waddell PJ, Hillis DM, Moritz C, Mable BK (1996) Mol Syst 407-514
-
(1996)
Mol Syst 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
Moritz, C.5
Mable, B.K.6
-
27
-
-
33646489947
-
Heterotachy in mammalian promoter evolution
-
Taylor MS, Kai C, Kawai J, Carninci P, Hayashizaki Y, Semple CA (2006) Heterotachy in mammalian promoter evolution. PLoS Genet 2:e30
-
(2006)
PLoS Genet
, vol.2
-
-
Taylor, M.S.1
Kai, C.2
Kawai, J.3
Carninci, P.4
Hayashizaki, Y.5
Semple, C.A.6
-
28
-
-
0031986279
-
Modeling the covarion hypothesis of nucleotide substitution
-
Tuffley C, Steel M (1998) Modeling the covarion hypothesis of nucleotide substitution. Math Biosci 147:63-91
-
(1998)
Math Biosci
, vol.147
, pp. 63-91
-
-
Tuffley, C.1
Steel, M.2
-
29
-
-
47749155531
-
Phylogenetic mixture models can reduce the node-density artifact
-
in press 2008
-
Venditti C, Meade A, Pagel M (2008) Phylogenetic mixture models can reduce the node-density artifact. Syst Biol, in press 2008
-
(2008)
Syst Biol
-
-
Venditti, C.1
Meade, A.2
Pagel, M.3
-
30
-
-
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
-
(1994)
J Mol Evol
, vol.39
, pp. 306-314
-
-
Yang, Z.1
|