-
1
-
-
0037329391
-
Bayes or bootstrap? a simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
-
M.E. Alfaro, S. Zoller, and F. Lutzoni Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence Mol. Biol. Evol. 20 2003 255 266
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 255-266
-
-
Alfaro, M.E.1
Zoller, S.2
Lutzoni, F.3
-
2
-
-
0037102484
-
Phylogenetic relationships of Pleuronectiformes based on molecular evidence
-
P.B. Berendzen, and W.W. Dimmick Phylogenetic relationships of Pleuronectiformes based on molecular evidence Copeia 3 2002 642 652
-
(2002)
Copeia
, vol.3
, pp. 642-652
-
-
Berendzen, P.B.1
Dimmick, W.W.2
-
3
-
-
12044249534
-
Probabilities of evolutionary trees
-
J.K.M. Brown Probabilities of evolutionary trees Syst. Biol. 43 1994 78 91
-
(1994)
Syst. Biol.
, vol.43
, pp. 78-91
-
-
Brown, J.K.M.1
-
4
-
-
0037242926
-
Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence
-
C.J. Cox, and T.A.J. Hedderson Phylogenetic relationships within the moss family Bryaceae based on chloroplast DNA evidence J. Bryol. 25 2003 31 40
-
(2003)
J. Bryol.
, vol.25
, pp. 31-40
-
-
Cox, C.J.1
Hedderson, T.A.J.2
-
5
-
-
0042069655
-
Comparing bootstrap and posterior probability values in the four-taxon case
-
M.P. Cummings, S.A. Handley, D.S. Myers, D.L. Reed, A. Rokas, and K. Winka Comparing bootstrap and posterior probability values in the four-taxon case Syst. Biol. 52 2003 477 487
-
(2003)
Syst. Biol.
, vol.52
, pp. 477-487
-
-
Cummings, M.P.1
Handley, S.A.2
Myers, D.S.3
Reed, D.L.4
Rokas, A.5
Winka, K.6
-
6
-
-
0037291495
-
Phylogeny of eusocial Lasioglossum reveals multiple losses of eusociality within a primitively eusocial clade of bees (Hymenoptera:Halictidae)
-
B.N. Danforth, L. Conway, and S.Q. Ji Phylogeny of eusocial Lasioglossum reveals multiple losses of eusociality within a primitively eusocial clade of bees (Hymenoptera:Halictidae) Syst. Biol. 52 2003 23 36
-
(2003)
Syst. Biol.
, vol.52
, pp. 23-36
-
-
Danforth, B.N.1
Conway, L.2
Ji, S.Q.3
-
7
-
-
0036792101
-
Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting
-
F. Delsuc, M. Scally, O. Madsen, M.J. Stanhope, W.W. de Jong, F.M. Catzeflis, M.S. Springer, and E.J.P. Douzery Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting Mol. Biol. Evol. 19 2002 1656 1671
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1656-1671
-
-
Delsuc, F.1
Scally, M.2
Madsen, O.3
Stanhope, M.J.4
De Jong, W.W.5
Catzeflis, F.M.6
Springer, M.S.7
Douzery, E.J.P.8
-
8
-
-
0037329108
-
Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability
-
C.J. Douady, F. Delsuc, Y. Boucher, W.F. Doolittle, and E.J.P. Douzery Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability Mol. Biol. Evol. 20 2003 248 254
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 248-254
-
-
Douady, C.J.1
Delsuc, F.2
Boucher, Y.3
Doolittle, W.F.4
Douzery, E.J.P.5
-
9
-
-
0004128472
-
-
Johns Hopkins University Press Baltimore, MD
-
A.W.F. Edwards Likelihood 1992 Johns Hopkins University Press Baltimore, MD
-
(1992)
Likelihood
-
-
Edwards, A.W.F.1
-
11
-
-
0242487486
-
Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics
-
P. Erixon, B. Svennblad, T. Britton, and B. Oxelman Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics Syst. Biol. 52 2003 665 673
-
(2003)
Syst. Biol.
, vol.52
, pp. 665-673
-
-
Erixon, P.1
Svennblad, B.2
Britton, T.3
Oxelman, B.4
-
12
-
-
84959807796
-
A probability model for inferring evolutionary trees
-
J.S. Farris A probability model for inferring evolutionary trees Syst. Zool. 22 1973 250 256
-
(1973)
Syst. Zool.
, vol.22
, pp. 250-256
-
-
Farris, J.S.1
-
13
-
-
0030417648
-
Parsimony jackknifing outperforms neighbor-joining
-
J.S. Farris, V.A. Albert, M. Källersjö, D. Lipscomb, and A. Kluge Parsimony jackknifing outperforms neighbor-joining Cladistics 12 1996 99 124
-
(1996)
Cladistics
, vol.12
, pp. 99-124
-
-
Farris, J.S.1
Albert, V.A.2
Källersjö, M.3
Lipscomb, D.4
Kluge, A.5
-
14
-
-
84959792503
-
The number of evolutionary trees
-
J. Felsenstein The number of evolutionary trees Syst. Zool. 27 1978 27 33
-
(1978)
Syst. Zool.
, vol.27
, pp. 27-33
-
-
Felsenstein, J.1
-
15
-
-
9744225587
-
Resurrecting logical probability
-
J. Franklin Resurrecting logical probability Erkenntnis 55 2001 277 305
-
(2001)
Erkenntnis
, vol.55
, pp. 277-305
-
-
Franklin, J.1
-
16
-
-
1642464904
-
An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy
-
J.V. Freudenstein, C. van den Berg, and M.W. Chase An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy Am. J. Bot. 91 2004 149 157
-
(2004)
Am. J. Bot.
, vol.91
, pp. 149-157
-
-
Freudenstein, J.V.1
Van Den Berg, C.2
Chase, M.W.3
-
17
-
-
0031848441
-
From star charts to stoneflies: Detecting relationships in continuous bivariate data
-
J.E. Garvey, E.A. Marschall, and R.A. Wright From star charts to stoneflies: detecting relationships in continuous bivariate data Ecology 79 1998 442 447
-
(1998)
Ecology
, vol.79
, pp. 442-447
-
-
Garvey, J.E.1
Marschall, E.A.2
Wright, R.A.3
-
18
-
-
0040696293
-
A Bayesian probability view of phylogenetic systematics
-
C.W. Harper A Bayesian probability view of phylogenetic systematics Syst. Zool. 28 1979 547 553
-
(1979)
Syst. Zool.
, vol.28
, pp. 547-553
-
-
Harper, C.W.1
-
19
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
W.K. Hastings Monte Carlo sampling methods using Markov chains and their applications Biometrika 57 1970 97 109
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.K.1
-
20
-
-
0037379673
-
Phylogeny estimation: Traditional and Bayesian approaches
-
M. Holder, and P.O. Lewis Phylogeny estimation: traditional and Bayesian approaches Nat. Rev. Genet. 4 2003 275 284
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 275-284
-
-
Holder, M.1
Lewis, P.O.2
-
21
-
-
0036005522
-
Geographic origin of human mitochondrial DNA: Accommodating phylogenetic uncertainty and model comparison
-
J.P. Huelsenbeck, and N.S. Imennov Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparison Syst. Biol. 51 2002 152 163
-
(2002)
Syst. Biol.
, vol.51
, pp. 152-163
-
-
Huelsenbeck, J.P.1
Imennov, N.S.2
-
22
-
-
0029821511
-
Do phylogenetic methods produce trees with biased shapes?
-
J.P. Huelsenbeck, and M. Kirkpatrick Do phylogenetic methods produce trees with biased shapes? Evolution 50 1996 1418 1424
-
(1996)
Evolution
, vol.50
, pp. 1418-1424
-
-
Huelsenbeck, J.P.1
Kirkpatrick, M.2
-
23
-
-
0036806280
-
Potential applications and pitfalls of Bayesian inference of phylogeny
-
J.P. Huelsenbeck, B. Larget, R.E. Miller, and F. Ronquist Potential applications and pitfalls of Bayesian inference of phylogeny Syst. Biol. 51 2002 673 688
-
(2002)
Syst. Biol.
, vol.51
, pp. 673-688
-
-
Huelsenbeck, J.P.1
Larget, B.2
Miller, R.E.3
Ronquist, F.4
-
24
-
-
0034849408
-
MrBayes: Bayesian inference of phylogenetic trees
-
J.P. Huelsenbeck, and F. Ronquist MrBayes: Bayesian inference of phylogenetic trees Biometrics 17 2001 754 755
-
(2001)
Biometrics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
25
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
J.P. Huelsenbeck, F. Ronquist, R. Nielsen, and J.P. Bollback Bayesian inference of phylogeny and its impact on evolutionary biology Science 294 2001 2310 2314
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
26
-
-
84862480886
-
Basal actinopterygian relationships: A mitogenomic perspective on the phylogeny of the "ancient fish"
-
J.G. Inoue, M. Miya, K. Tsukamoto, and M. Nishida Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish" Integr. Comp. Biol. 42 2002 1249 1249
-
(2002)
Integr. Comp. Biol.
, vol.42
, pp. 1249-1249
-
-
Inoue, J.G.1
Miya, M.2
Tsukamoto, K.3
Nishida, M.4
-
27
-
-
0037291474
-
Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion (Odonata:Coenagrionidae)
-
S. Jordan, C. Simon, and D. Polhemus Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion (Odonata: Coenagrionidae) Syst. Biol. 52 2003 89 109
-
(2003)
Syst. Biol.
, vol.52
, pp. 89-109
-
-
Jordan, S.1
Simon, C.2
Polhemus, D.3
-
28
-
-
0030327756
-
The selection of prior distributions by formal rules
-
R.E. Kass, and L. Wasserman The selection of prior distributions by formal rules J. Am. Stat. Assoc. 91 1996 1343 1370
-
(1996)
J. Am. Stat. Assoc.
, vol.91
, pp. 1343-1370
-
-
Kass, R.E.1
Wasserman, L.2
-
29
-
-
0036436267
-
Conflicting molecular phylogenies of European long-eared bats (Plecotus) can be explained by cryptic diversity
-
A. Kiefer, F. Mayer, J. Kosuch, O. von Helversen, and A. Veith Conflicting molecular phylogenies of European long-eared bats (Plecotus) can be explained by cryptic diversity Mol. Phylogenet. Evol. 25 2002 557 566
-
(2002)
Mol. Phylogenet. Evol.
, vol.25
, pp. 557-566
-
-
Kiefer, A.1
Mayer, F.2
Kosuch, J.3
Von Helversen, O.4
Veith, A.5
-
30
-
-
0035180894
-
Selagineae and Manuleeae, two tribes or one? Phylogenetic studies in the Scrophulariaceae
-
P. Kornhall, N. Heidari, and B. Bremer Selagineae and Manuleeae, two tribes or one? Phylogenetic studies in the Scrophulariaceae Plant Syst. Evol. 228 2001 199 218
-
(2001)
Plant Syst. Evol.
, vol.228
, pp. 199-218
-
-
Kornhall, P.1
Heidari, N.2
Bremer, B.3
-
31
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
B. Larget, and D.L. Simon Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees Mol. Biol. Evol. 16 1999 750 759
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 750-759
-
-
Larget, B.1
Simon, D.L.2
-
32
-
-
0036005516
-
Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches
-
A.D. Leache, and T.W. Reeder Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of parsimony, likelihood, and Bayesian approaches Syst. Biol. 51 2002 44 68
-
(2002)
Syst. Biol.
, vol.51
, pp. 44-68
-
-
Leache, A.D.1
Reeder, T.W.2
-
33
-
-
0035145155
-
Phylogenetic systematics turns over a new leaf
-
P.O. Lewis Phylogenetic systematics turns over a new leaf Trends Ecol. Evol. 16 2001 30 37
-
(2001)
Trends Ecol. Evol.
, vol.16
, pp. 30-37
-
-
Lewis, P.O.1
-
35
-
-
0035987401
-
Historical biogeography of the livebearing fish genus Poeciliopsis (Poeciliidae:Cyprinodontiformes)
-
M. Mateos, O.I. Sanjur, and R.C. Vrijenhoek Historical biogeography of the livebearing fish genus Poeciliopsis (Poeciliidae:Cyprinodontiformes) Evolution 56 2002 972 984
-
(2002)
Evolution
, vol.56
, pp. 972-984
-
-
Mateos, M.1
Sanjur, O.I.2
Vrijenhoek, R.C.3
-
37
-
-
5744249209
-
Equations of state calculations by fast computing machines
-
N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, and E. Teller Equations of state calculations by fast computing machines J. Chem. Phys. 21 1953 1087 1092
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
38
-
-
0036037993
-
Phylogenetic analysis and a test of the current infrageneric classification of Norops (beta Anolis)
-
K.E. Nicholson Phylogenetic analysis and a test of the current infrageneric classification of Norops (beta Anolis) Herpetol. Monogr. 16 2002 93 120
-
(2002)
Herpetol. Monogr.
, vol.16
, pp. 93-120
-
-
Nicholson, K.E.1
-
39
-
-
0031773680
-
Modeltest: Testing the model of DNA substitution
-
D. Posada, and K.A. Crandall Modeltest: testing the model of DNA substitution Bioinformatics 14 1998 817 818
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
40
-
-
0029818407
-
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
-
B. Rannala, and Z.H. Yang Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference J. Mol. Evol. 43 1996 304 311
-
(1996)
J. Mol. Evol.
, vol.43
, pp. 304-311
-
-
Rannala, B.1
Yang, Z.H.2
-
41
-
-
0036019715
-
Molecular systematics of the Jacks (Perciformes:Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches
-
D.L. Reed, K.E. Carpenter, and M.J. deGravelle Molecular systematics of the Jacks (Perciformes:Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches Mol. Phylogenet. Evol. 23 2002 513 524
-
(2002)
Mol. Phylogenet. Evol.
, vol.23
, pp. 513-524
-
-
Reed, D.L.1
Carpenter, K.E.2
Degravelle, M.J.3
-
42
-
-
12244276365
-
Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera:Cynipidae:Cynipini) using mitochondrial sequence data
-
A. Rokas, G. Melika, Y. Abe, J.L. Nieves-Aldrey, J.M. Cook, and G.N. Stone Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera:Cynipidae:Cynipini) using mitochondrial sequence data Mol. Phylogenet. Evol. 26 2003 36 45
-
(2003)
Mol. Phylogenet. Evol.
, vol.26
, pp. 36-45
-
-
Rokas, A.1
Melika, G.2
Abe, Y.3
Nieves-Aldrey, J.L.4
Cook, J.M.5
Stone, G.N.6
-
43
-
-
0036821739
-
Taxon sampling and seed plant phylogeny
-
C. Rydin, and M. Källersjö Taxon sampling and seed plant phylogeny Cladistics 18 2002 485 513
-
(2002)
Cladistics
, vol.18
, pp. 485-513
-
-
Rydin, C.1
Källersjö, M.2
-
44
-
-
0034351392
-
Improved bootstrap confidence limits in large-scale phylogenies, with and example from Neoastragalus (Leguminosae)
-
M.J. Sanderson, and M.F. Wojciechowski Improved bootstrap confidence limits in large-scale phylogenies, with and example from Neoastragalus (Leguminosae) Syst. Biol. 49 2000 671 685
-
(2000)
Syst. Biol.
, vol.49
, pp. 671-685
-
-
Sanderson, M.J.1
Wojciechowski, M.F.2
-
46
-
-
0037058983
-
Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
-
Y. Suzuki, G.V. Glazko, and M. Nei Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics Proc. Natl. Acad. Sci. USA 99 2002 16138 16143
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16138-16143
-
-
Suzuki, Y.1
Glazko, G.V.2
Nei, M.3
-
48
-
-
0001336205
-
Phylogenetic inference
-
D.M. Hillis C. Moritz B.K. Mable Sinauer Associates Sunderland, MA
-
D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis Phylogenetic inference D.M. Hillis C. Moritz B.K Mable Molecular Systematics 1996 Sinauer Associates Sunderland, MA 407 514
-
(1996)
Molecular Systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
49
-
-
0000576595
-
Markov chains for exploring posterior distributions
-
L. Tierney Markov chains for exploring posterior distributions Ann. Stat. 4 1994 1701 1762
-
(1994)
Ann. Stat.
, vol.4
, pp. 1701-1762
-
-
Tierney, L.1
-
50
-
-
0031149251
-
Links between maximum likelihood and maximum parsimony under a simple model of site substitution
-
C. Tuffley, and M. Steel Links between maximum likelihood and maximum parsimony under a simple model of site substitution B. Math. Biol. 59 1997 1 18
-
(1997)
B. Math. Biol.
, vol.59
, pp. 1-18
-
-
Tuffley, C.1
Steel, M.2
-
51
-
-
0037207217
-
Phylogenetic relationships of the Oriental-Australian rear-fanged water snakes (Colubridae:Homalopsinae) based on mitochondrial DNA sequences
-
H.K. Voris, M.E. Alfaro, D.R. Karns, G.L. Starnes, E. Thompson, and J.C. Murphy Phylogenetic relationships of the Oriental-Australian rear-fanged water snakes (Colubridae:Homalopsinae) based on mitochondrial DNA sequences Copeia 4 2002 906 915
-
(2002)
Copeia
, vol.4
, pp. 906-915
-
-
Voris, H.K.1
Alfaro, M.E.2
Karns, D.R.3
Starnes, G.L.4
Thompson, E.5
Murphy, J.C.6
-
52
-
-
0001907991
-
Inferences from multinomial data: Learning about a bag of marbles
-
P. Walley Inferences from multinomial data: learning about a bag of marbles J. Roy. Stat. Soc. B Met. 58 1996 3 34
-
(1996)
J. Roy. Stat. Soc. B Met.
, vol.58
, pp. 3-34
-
-
Walley, P.1
-
54
-
-
0011166878
-
Congruence among data sets: A Bayesian approach
-
M.M. Miyamoto J. Cracraft Oxford University Press Oxford
-
W.C. Wheeler Congruence among data sets: a Bayesian approach M.M. Miyamoto J. Cracraft Phylogenetic Analysis of DNA Sequences 1991 Oxford University Press Oxford 334 346
-
(1991)
Phylogenetic Analysis of DNA Sequences
, pp. 334-346
-
-
Wheeler, W.C.1
-
55
-
-
0036431235
-
Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
-
T.P. Wilcox, D.J. Zwickl, T.A. Heath, and D.M. Hillis Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support Mol. Phylogenet. Evol. 25 2002 361 371
-
(2002)
Mol. Phylogenet. Evol.
, vol.25
, pp. 361-371
-
-
Wilcox, T.P.1
Zwickl, D.J.2
Heath, T.A.3
Hillis, D.M.4
|