-
1
-
-
14544289241
-
Accounting for uncertainty in the tree topology has little effect on the decision theoretic approach to model selection in phylogeny estimation
-
Abdo Z, Minin V, Joyce P, Sullivan J. 2005. Accounting for uncertainty in the tree topology has little effect on the decision theoretic approach to model selection in phylogeny estimation. Mol. Biol. Evol. 22:691-703
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 691-703
-
-
Abdo, Z.1
Minin, V.2
Joyce, P.3
Sullivan, J.4
-
2
-
-
0000501656
-
Information theory and an extension of the maximum likelihood principle
-
ed. PN Petrov, F Csaki Budapest: Akad. Kiado
-
Akaike H. 1973. Information theory and an extension of the maximum likelihood principle. In Second International Symposium on Information Theory, ed. PN Petrov, F Csaki. pp. 267-81. Budapest: Akad. Kiado
-
(1973)
Second International Symposium on Information Theory
, pp. 267-281
-
-
Akaike, H.1
-
3
-
-
4444220955
-
Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA
-
Anderson FE, Swofford DL. 2004. Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol. Phylogenet. Evol. 33:440-51
-
(2004)
Mol. Phylogenet. Evol.
, vol.33
, pp. 440-451
-
-
Anderson, F.E.1
Swofford, D.L.2
-
4
-
-
0035986890
-
Bayesian model adequacy and choice in phylogenetics
-
Bollback JP. 2002. Bayesian model adequacy and choice in phylogenetics. Mol. Biol. Evol. 19:1171-80
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1171-1180
-
-
Bollback, J.P.1
-
5
-
-
0000025871
-
Science and statistics
-
Box GEP. 1976. Science and statistics. J. Am. Stat. Assoc. 71:791-99
-
(1976)
J. Am. Stat. Assoc.
, vol.71
, pp. 791-799
-
-
Box, G.E.P.1
-
7
-
-
0032927161
-
Topological bias and inconsistency of maximum likelihood using wrong models
-
Bruno WJ, Halpern AL. 1999. Topological bias and inconsistency of maximum likelihood using wrong models. Mol. Biol. Evol. 16:564-66
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 564-566
-
-
Bruno, W.J.1
Halpern, A.L.2
-
8
-
-
0036623259
-
Model misspecification and probabilistic tests of topology: Evidence from empirical data sets
-
Buckley TR. 2002. Model misspecification and probabilistic tests of topology: evidence from empirical data sets. Syst. Biol. 51:509-23
-
(2002)
Syst. Biol.
, vol.51
, pp. 509-523
-
-
Buckley, T.R.1
-
9
-
-
0036213207
-
The effects of nucleotide substitution model assumptions on estimates of non-parametric bootstrap support
-
Buckley TR, Cunningham CW. 2002. The effects of nucleotide substitution model assumptions on estimates of non-parametric bootstrap support. Mol. Biol. Evol. 19:394-405
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 394-405
-
-
Buckley, T.R.1
Cunningham, C.W.2
-
10
-
-
0035527383
-
Exploring among-site rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths, and bootstrap support
-
Buckley TR, Simon C, Chambers GC. 2001. Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Syst. Biol. 50:67-86
-
(2001)
Syst. Biol.
, vol.50
, pp. 67-86
-
-
Buckley, T.R.1
Simon, C.2
Chambers, G.C.3
-
12
-
-
8744307994
-
Multi-model inference: Understanding AIC and BIC in model selection
-
Burnham KP, Anderson DA. 2004. Multi-model inference: understanding AIC and BIC in model selection. Sociol. Method Res. 33:261-304
-
(2004)
Sociol. Method Res.
, vol.33
, pp. 261-304
-
-
Burnham, K.P.1
Anderson, D.A.2
-
13
-
-
9644272771
-
Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group
-
Carstens BC, Stevenson AL, Degenhardt JD, Sullivan J. 2004. Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group. Syst. Biol. 53:781-92
-
(2004)
Syst. Biol.
, vol.53
, pp. 781-792
-
-
Carstens, B.C.1
Stevenson, A.L.2
Degenhardt, J.D.3
Sullivan, J.4
-
14
-
-
3242695950
-
Data partitions and complex models in Bayesian analysis: The phylogeny of gymnophthalmid lizards
-
Castoe TA, Doan TM, Parkinson CL. 2004. Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophthalmid lizards. Syst. Biol. 53:448-59
-
(2004)
Syst. Biol.
, vol.53
, pp. 448-459
-
-
Castoe, T.A.1
Doan, T.M.2
Parkinson, C.L.3
-
15
-
-
0036368312
-
Phylogeny and character evolution in the Empidonax group of tyrant flycatchers (Aves: Tyrannidae): A test of W.E. Lanyon's hypothesis using mtDNA sequences
-
Cicero C, Johnson N. 2001. Phylogeny and character evolution in the Empidonax group of tyrant flycatchers (Aves: Tyrannidae): a test of W.E. Lanyon's hypothesis using mtDNA sequences. Mol. Phylogenet. Evol. 22:289-302
-
(2001)
Mol. Phylogenet. Evol.
, vol.22
, pp. 289-302
-
-
Cicero, C.1
Johnson, N.2
-
16
-
-
0031713421
-
Best-fit maximum likelihood models for phylogenetic inference: Empirical tests with known phylogenies
-
Cunningham CW, Zhu H, Hillis DM. 1998. Best-fit maximum likelihood models for phylogenetic inference: empirical tests with known phylogenies. Evolution 52:978-87
-
(1998)
Evolution
, vol.52
, pp. 978-987
-
-
Cunningham, C.W.1
Zhu, H.2
Hillis, D.M.3
-
17
-
-
0037356657
-
Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwestern North America
-
Demboski JR, Sullivan J. 2003. Extensive mtDNA variation within the yellow-pine chipmunk, Tamias amoenus (Rodentia: Sciuridae), and phylogeographic inferences for northwestern North America. Mol. Phylogenet. Evol. 26:389-408
-
(2003)
Mol. Phylogenet. Evol.
, vol.26
, pp. 389-408
-
-
Demboski, J.R.1
Sullivan, J.2
-
18
-
-
0242487486
-
Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics
-
Erixon P, Svennblad B, Britton T, Oxelman B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52:665-73
-
(2003)
Syst. Biol.
, vol.52
, pp. 665-673
-
-
Erixon, P.1
Svennblad, B.2
Britton, T.3
Oxelman, B.4
-
19
-
-
84959798530
-
Cases in which parsimony and compatibility methods will be positively misleading
-
Felsenstein J. 1978. Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool. 27:401-10
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
20
-
-
0034818755
-
Taking variation of evolutionary rates between sites into account in inferring phylogenies
-
Felsenstein J. 2001. Taking variation of evolutionary rates between sites into account in inferring phylogenies. J. Mol. Evol. 53:447-55
-
(2001)
J. Mol. Evol.
, vol.53
, pp. 447-455
-
-
Felsenstein, J.1
-
23
-
-
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. 4:579-93
-
(1970)
Biochem. Genet.
, vol.4
, pp. 579-593
-
-
Fitch, W.M.1
Markowitz, E.2
-
24
-
-
3242701529
-
Modeling compositional heterogeneity
-
Foster PG. 2004. Modeling compositional heterogeneity. Syst. Biol. 53:485-95
-
(2004)
Syst. Biol.
, vol.53
, pp. 485-495
-
-
Foster, P.G.1
-
26
-
-
0035029534
-
Maximum-likelihood phylogenetic analysis underacovarion-like model
-
Galtier N. 2001. Maximum-likelihood phylogenetic analysis underacovarion-like model. Mol. Biol. Evol. 18:866-73
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 866-873
-
-
Galtier, N.1
-
27
-
-
0031829758
-
Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
-
Galtier N, Guoy M. 1998. Inferring pattern and process: maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol. Biol. Evol. 15:871-79
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 871-879
-
-
Galtier, N.1
Guoy, M.2
-
28
-
-
0028887457
-
Success of maximum likelihood phylogeny inference in the four-taxon case
-
Gaut BS, Lewis PO. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12:152-62
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 152-162
-
-
Gaut, B.S.1
Lewis, P.O.2
-
29
-
-
0008114066
-
Rates of molecular evolution
-
Gillespie JH. 1986. Rates of molecular evolution. Annu. Rev. Ecol. Syst. 17:636-65
-
(1986)
Annu. Rev. Ecol. Syst.
, vol.17
, pp. 636-665
-
-
Gillespie, J.H.1
-
30
-
-
0021003230
-
Estimates of DNA and protein sequence divergence: An examination of some assumptions
-
Golding GB. 1983. Estimates of DNA and protein sequence divergence: an examination of some assumptions. Mol. Biol. Evol. 1:125-42
-
(1983)
Mol. Biol. Evol.
, vol.1
, pp. 125-142
-
-
Golding, G.B.1
-
31
-
-
0027526039
-
Statistical tests of models of DNA substitution
-
Goldman N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-98
-
(1993)
J. Mol. Evol.
, vol.36
, pp. 182-198
-
-
Goldman, N.1
-
32
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman N, Yang Z. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:511-23
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 511-523
-
-
Goldman, N.1
Yang, Z.2
-
33
-
-
0029068893
-
Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
-
Gu X, Fu YX, Li WH. 1995. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol. Biol. Evol. 12:546-57
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 546-557
-
-
Gu, X.1
Fu, Y.X.2
Li, W.H.3
-
34
-
-
0031875569
-
Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
-
Halpern A, Bruno WJ. 1998. Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol. Biol. Evol. 15:910-17
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 910-917
-
-
Halpern, A.1
Bruno, W.J.2
-
35
-
-
11144352825
-
Molecular phylogeny of the superfamily Tephritoidea (Insecta: Diptera): new evidence from the mitochondrial 12S, 16S, and COII genes
-
Han HY, Ro KE. 2005. Molecular phylogeny of the superfamily Tephritoidea (Insecta: Diptera): new evidence from the mitochondrial 12S, 16S, and COII genes. Mol. Phylogenet. Evol. 34:416-30
-
(2005)
Mol. Phylogenet. Evol.
, vol.34
, pp. 416-430
-
-
Han, H.Y.1
Ro, K.E.2
-
36
-
-
0025086910
-
Phylogeny and molecular evolution of primates
-
Hasegawa M. 1990. Phylogeny and molecular evolution of primates. Jpn. J. Genet. 65:243-65
-
(1990)
Jpn. J. Genet.
, vol.65
, pp. 243-265
-
-
Hasegawa, M.1
-
37
-
-
0022376704
-
Dating the human-ape split by a molecular clock of mitochondrial DNA
-
Hasegawa M, Kishino H, Yano T. 1985. Dating the human-ape split by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22:160-74
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
38
-
-
0036097894
-
Testing a covariotide model of DNA substitution
-
Hueslenbeck JP. 2002. Testing a covariotide model of DNA substitution. Mol. Biol. Evol. 19:698-707
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 698-707
-
-
Hueslenbeck, J.P.1
-
39
-
-
0031436890
-
Phylogeny estimation and hypothesis testing using maximum likelihood
-
Huelsenbeck JP, Crandall KA. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-66
-
(1997)
Annu. Rev. Ecol. Syst.
, vol.28
, pp. 437-466
-
-
Huelsenbeck, J.P.1
Crandall, K.A.2
-
40
-
-
12044255023
-
Success of phylogenetic methods in the four-taxon case
-
Huelsenbeck JP, Hillis DM. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-64
-
(1993)
Syst. Biol.
, vol.42
, pp. 247-264
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
41
-
-
11144277878
-
Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
-
Huelsenbeck JP, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 904-13
-
(2004)
Syst. Biol.
, pp. 904-913
-
-
Huelsenbeck, J.P.1
Rannala, B.2
-
42
-
-
0034849408
-
MR-BAYES: Bayesian inference of phylogeny
-
Huelsenbeck JP, Ronquist F. 2001. MR-BAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-55
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
43
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-14
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
44
-
-
2442671519
-
Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
-
Huelsenbeck JP, Larget B, Alfaro M. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21:1123-33
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1123-1133
-
-
Huelsenbeck, J.P.1
Larget, B.2
Alfaro, M.3
-
45
-
-
1242296549
-
Model selection in ecology and evolution
-
Johnson JP, Omland KS. 2004. Model selection in ecology and evolution. Trends Ecol. Evol. 19:101-08
-
(2004)
Trends Ecol. Evol.
, vol.19
, pp. 101-108
-
-
Johnson, J.P.1
Omland, K.S.2
-
46
-
-
0000732090
-
Evolution of protein molecules
-
ed. N Munro, New York: Academic
-
Jukes TH, Cantor CR. 1969. Evolution of protein molecules. In Mammalian Protein Metabolism, ed. N Munro, pp. 21-132. New York: Academic
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
48
-
-
0019296687
-
A simple model for estimating evolutionary rates of base substitutions between homologous nucleotide sequences
-
Kimura M. 1980. A simple model for estimating evolutionary rates of base substitutions between homologous nucleotide sequences. J. Mol. Evol. 16:111-20
-
(1980)
J. Mol. Evol.
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
49
-
-
3242721251
-
Aligned 18S and insect phylogeny
-
Kjer K. 2004. Aligned 18S and insect phylogeny. Syst. Biol. 53:506-14
-
(2004)
Syst. Biol.
, vol.53
, pp. 506-514
-
-
Kjer, K.1
-
50
-
-
2442581218
-
The importance of proper model assumption in Bayesian phylogenetics
-
Lemmon AR, Moriarty EC. 2004. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol. 53:265-77
-
(2004)
Syst. Biol.
, vol.53
, pp. 265-277
-
-
Lemmon, A.R.1
Moriarty, E.C.2
-
51
-
-
9744238911
-
Molecular phylogeny and evidence for an adaptive radiation of geophagine cichlids from South America (Perciformes: Labroidei)
-
López-Fernández H, Honeycutt RL, Winemiller KO. 2005. Molecular phylogeny and evidence for an adaptive radiation of geophagine cichlids from South America (Perciformes: Labroidei). Mol. Phylogenet. Evol. 34:227-44
-
(2005)
Mol. Phylogenet. Evol.
, vol.34
, pp. 227-244
-
-
López-Fernández, H.1
Honeycutt, R.L.2
Winemiller, K.O.3
-
52
-
-
0037195104
-
Molecular evidence of HIV-1 transmission in a criminal case
-
Metzker ML, Mindell DP, Liu X, Ptak RG, Gibbs RA, Hillis DM. 2002. Molecular evidence of HIV-1 transmission in a criminal case. Proc. Natl. Acad. Sci. USA 99:14293-97
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14293-14297
-
-
Metzker, M.L.1
Mindell, D.P.2
Liu, X.3
Ptak, R.G.4
Gibbs, R.A.5
Hillis, D.M.6
-
53
-
-
0242487488
-
Performance-based selection of likelihood models for phylogeny estimation
-
Minin V, Abdo Z, Joyce P, Sullivan J. 2003. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol. 52:674-83
-
(2003)
Syst. Biol.
, vol.52
, pp. 674-683
-
-
Minin, V.1
Abdo, Z.2
Joyce, P.3
Sullivan, J.4
-
54
-
-
0028024626
-
A likelihood approach for comparing synonymous and non-synonymous nucleotide substitutions rates, with application to the chloroplast genome
-
Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and non-synonymous nucleotide substitutions rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:1139-51
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 1139-1151
-
-
Muse, S.V.1
Gaut, B.S.2
-
56
-
-
12444319405
-
Empirical problems of the hierarchical likelihood ratio test for model selection
-
Pol D. 2004. Empirical problems of the hierarchical likelihood ratio test for model selection. Syst. Biol. 53:949-62
-
(2004)
Syst. Biol.
, vol.53
, pp. 949-962
-
-
Pol, D.1
-
57
-
-
9644301241
-
Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests
-
Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793-808
-
(2004)
Syst. Biol.
, vol.53
, pp. 793-808
-
-
Posada, D.1
Buckley, T.R.2
-
58
-
-
0031773680
-
Modeltest: Testing the model of DNA substitution
-
Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-18
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
59
-
-
0035527410
-
Selecting the best-fit model of nucleotide substitution
-
Posada D, Crandall KA. 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50:580-601
-
(2001)
Syst. Biol.
, vol.50
, pp. 580-601
-
-
Posada, D.1
Crandall, K.A.2
-
60
-
-
0001201909
-
Bayesian model selection in social research
-
with discussion by A Gelman, DB Rubin, and RM Hauser. ed. PV Marsden, Oxford, UK: Blackwell Sci.
-
Raftery AE. 1995. Bayesian model selection in social research (with discussion by A Gelman, DB Rubin, and RM Hauser). In Sociological Methodology, ed. PV Marsden, pp. 111-96. Oxford, UK: Blackwell Sci.
-
(1995)
Sociological Methodology
, pp. 111-196
-
-
Raftery, A.E.1
-
61
-
-
0000783674
-
Hypothesis testing and model selection
-
ed. WR Gilks, S Richardson, DJ Speigelhalter, New York: Chapman & Hall
-
Raftery AE. 1996. Hypothesis testing and model selection. In Markov Chain Monte Carlo in Practice, ed. WR Gilks, S Richardson, DJ Speigelhalter, pp. 163-87. New York: Chapman & Hall
-
(1996)
Markov Chain Monte Carlo in Practice
, pp. 163-187
-
-
Raftery, A.E.1
-
62
-
-
0036803348
-
Identifiability of parameters in MCMC Bayesian inference of phylogeny
-
Rannala B. 2002. Identifiability of parameters in MCMC Bayesian inference of phylogeny. Syst. Biol. 51:754-60
-
(2002)
Syst. Biol.
, vol.51
, pp. 754-760
-
-
Rannala, B.1
-
63
-
-
0034351397
-
Parametric phylogenetics?
-
Sanderson MJ, Kim J. 2000. Parametric phylogenetics? Syst. Biol. 49:817-29
-
(2000)
Syst. Biol.
, vol.49
, pp. 817-829
-
-
Sanderson, M.J.1
Kim, J.2
-
64
-
-
0000120766
-
Estimating the dimensions of a model
-
Schwarz G. 1978. Estimating the dimensions of a model. Ann. Stat. 6:461-64
-
(1978)
Ann. Stat.
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
65
-
-
0000215283
-
Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris zone
-
Siddall ME. 1998. Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris zone. Cladistics 14:209-20
-
(1998)
Cladistics
, vol.14
, pp. 209-220
-
-
Siddall, M.E.1
-
66
-
-
0344430832
-
Probabilism and phylogenetic inference
-
Siddall ME, Kluge AG. 1997. Probabilism and phylogenetic inference. Cladistics 13:313-36
-
(1997)
Cladistics
, vol.13
, pp. 313-336
-
-
Siddall, M.E.1
Kluge, A.G.2
-
68
-
-
0034983646
-
Bayesian selection of continuous-time Markov chain evolutionary models
-
Suchard MA, Weiss RE, Sinsheimer JS. 2002. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18:1001-13
-
(2002)
Mol. Biol. Evol.
, vol.18
, pp. 1001-1013
-
-
Suchard, M.A.1
Weiss, R.E.2
Sinsheimer, J.S.3
-
70
-
-
0002618746
-
Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics
-
Sullivan J, Swofford DL. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. J. Mammal. Evol. 4:77-86
-
(1997)
J. Mammal. Evol.
, vol.4
, pp. 77-86
-
-
Sullivan, J.1
Swofford, D.L.2
-
71
-
-
0035527373
-
Should we use model-based methods for phylogenetic inference when we know assumptions about among-site rate variation and nucleotide substitution pattern are violated?
-
Sullivan J, Swofford DL. 2001. Should we use model-based methods for phylogenetic inference when we know assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst. Biol. 50:723-29
-
(2001)
Syst. Biol.
, vol.50
, pp. 723-729
-
-
Sullivan, J.1
Swofford, D.L.2
-
72
-
-
0034091330
-
Comparative phylogeography of Mesoamerican highland rodents: Concerted versus independent responses to past climatic fluctuations
-
Sullivan J, Arellano EA, Rogers DS. 2000. Comparative phylogeography of Mesoamerican highland rodents: concerted versus independent responses to past climatic fluctuations. Am. Nat. 155:755-68
-
(2000)
Am. Nat.
, vol.155
, pp. 755-768
-
-
Sullivan, J.1
Arellano, E.A.2
Rogers, D.S.3
-
73
-
-
0029880314
-
The effect of topology on estimates of among-site rate variation
-
Sullivan J, Holsinger KE, Simon C. 1996. The effect of topology on estimates of among-site rate variation. J. Mol. Evol. 42:308-12
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 308-312
-
-
Sullivan, J.1
Holsinger, K.E.2
Simon, C.3
-
74
-
-
0031224772
-
Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood
-
Sullivan J, Markert JA, Kilpatrick CW. 1997. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Syst. Biol. 46:426-40
-
(1997)
Syst. Biol.
, vol.46
, pp. 426-440
-
-
Sullivan, J.1
Markert, J.A.2
Kilpatrick, C.W.3
-
75
-
-
0032875445
-
The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models
-
Sullivan J, Swofford DL, Naylor GJP. 1999. The effect of taxon sampling on estimating rate heterogeneity parameters of maximum-likelihood models. Mol. Biol. Evol. 16:1347-56
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1347-1356
-
-
Sullivan, J.1
Swofford, D.L.2
Naylor, G.J.P.3
-
77
-
-
0346952694
-
Phylogenetic inference using parsimony and maximum likelihood using PAUP*
-
ed. M Salemi, AM Vandamme, Cambridge, UK: Cambridge Univ. Press
-
Swofford DL, Sullivan J. 2003. Phylogenetic inference using parsimony and maximum likelihood using PAUP*. In The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny, ed. M Salemi, AM Vandamme, pp. 160-96. Cambridge, UK: Cambridge Univ. Press
-
(2003)
The Phylogenetic Handbook: A Practical Approach to DNA and Protein Phylogeny
, pp. 160-196
-
-
Swofford, D.L.1
Sullivan, J.2
-
78
-
-
0001336205
-
Phylogenetic inference
-
ed. DM Hillis, C Moritz, BK Mable, Sunderland, MA: Sinauer Assoc. 2nd ed
-
Swofford DL, Olsen GJ, Waddell PJ, Hillis DM. 1996. Phylogenetic inference. In Molecular Systematics, ed. DM Hillis, C Moritz, BK Mable, pp. 407-514. Sunderland, MA: Sinauer Assoc. 2nd ed
-
(1996)
Molecular Systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
79
-
-
0035527406
-
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
-
Swofford DL, Waddell PJ, Huelsenbeck JP, Foster PG, Lewis PO, Rogers JS. 2001. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50:525-39
-
(2001)
Syst. Biol.
, vol.50
, pp. 525-539
-
-
Swofford, D.L.1
Waddell, P.J.2
Huelsenbeck, J.P.3
Foster, P.G.4
Lewis, P.O.5
Rogers, J.S.6
-
80
-
-
0027157960
-
Estimation of the number of nucleotides substitutions in the control region of mitochondrial DNA in humans and chimpanzees
-
Tamura K, Nei M. 1993. Estimation of the number of nucleotides substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-26
-
(1993)
Mol. Biol. Evol.
, vol.10
, pp. 512-526
-
-
Tamura, K.1
Nei, M.2
-
81
-
-
0002671410
-
Some probabilistic and statistical problems in the analysis of DNA sequences
-
Tavaré S. 1986. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17:57-86
-
(1986)
Lect. Math. Life Sci.
, vol.17
, pp. 57-86
-
-
Tavaré, S.1
-
82
-
-
0028874337
-
Neighbor joining and maximum likelihood with RNA sequences: Addressing the interdependence of sites
-
Tillier ERM, Collins RA. 1995. Neighbor joining and maximum likelihood with RNA sequences: addressing the interdependence of sites. Mol. Biol. Evol. 12:7-15
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 7-15
-
-
Tillier, E.R.M.1
Collins, R.A.2
-
83
-
-
0031986279
-
Modeling the covarion hypothesis of nucleotide substitution
-
Tuffley C, Steele 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
Steele, M.2
-
84
-
-
0015219691
-
Fitting discrete probability distributions to evolutionary events
-
Uzzell T, Corbin KW. 1971. Fitting discrete probability distributions to evolutionary events. Science 172:1089-96
-
(1971)
Science
, vol.172
, pp. 1089-1096
-
-
Uzzell, T.1
Corbin, K.W.2
-
85
-
-
0002574561
-
Evolutionary trees of apes and humans from DNA sequences
-
ed. AJ Lock, CR Peters, Oxford: Clarendon
-
Waddell P, Penny D. 1996. Evolutionary trees of apes and humans from DNA sequences. In Handbook of Symbolic Evolution, ed. AJ Lock, CR Peters, pp. 53-73. Oxford: Clarendon
-
(1996)
Handbook of Symbolic Evolution
, pp. 53-73
-
-
Waddell, P.1
Penny, D.2
-
86
-
-
0035339920
-
Molecular phylogenetics: State of the art methods for looking into the past
-
Whelan S, Lio P, Goldman N. 2001. Molecular phylogenetics: state of the art methods for looking into the past. Trends Genet. 17:262-72
-
(2001)
Trends Genet.
, vol.17
, pp. 262-272
-
-
Whelan, S.1
Lio, P.2
Goldman, N.3
-
87
-
-
11144355733
-
Origin of AIDS: Contaminated polio vaccine theory refuted
-
Worobey M, Santiago ML, Keele BF, Ndjango JBN, Joy JB, Labamall BL, et al. 2004. Origin of AIDS: contaminated polio vaccine theory refuted. Nature 428:820
-
(2004)
Nature
, vol.428
, pp. 820
-
-
Worobey, M.1
Santiago, M.L.2
Keele, B.F.3
Ndjango, J.B.N.4
Joy, J.B.5
Labamall, B.L.6
-
88
-
-
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
-
(1993)
Mol. Biol. Evol.
, vol.10
, pp. 1396-1401
-
-
Yang, Z.1
-
89
-
-
0028214103
-
Estimating the pattern of nucleotide substitution
-
Yang Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-11
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 105-111
-
-
Yang, Z.1
-
90
-
-
0030638573
-
How often do wrong models produce better phylogenies?
-
Yang Z. 1997. How often do wrong models produce better phylogenies? Mol. Biol. Evol. 14:105-08
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 105-108
-
-
Yang, Z.1
-
91
-
-
0028961933
-
On the use of nucleic acid sequences to infer early branchings in the tree of life
-
Yang Z, Roberts D. 1995. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol. Biol. Evol. 12:451-58
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 451-458
-
-
Yang, Z.1
Roberts, D.2
|