-
1
-
-
0037329391
-
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
-
ALFARO, M. E., S. ZOLLER, AND F. LUTZONI. 2003. 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. 20:255-266.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 255-266
-
-
Alfaro, M.E.1
Zoller, S.2
Lutzoni, F.3
-
2
-
-
0032273615
-
General methods for monitoring convergence of iterative simulations
-
BROOKS, S. P., AND A. GELMAN. 1998. General methods for monitoring convergence of iterative simulations. J. Comput. Graph. Stat. 7:434-455.
-
(1998)
J. Comput. Graph. Stat.
, vol.7
, pp. 434-455
-
-
Brooks, S.P.1
Gelman, A.2
-
3
-
-
0036005521
-
Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera
-
BUCKLEY, T. R., P. ARENSBURGER, C. SIMON, AND G. K. CHAMBERS. 2002. Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst. Biol. 51:4-18.
-
(2002)
Syst. Biol.
, vol.51
, pp. 4-18
-
-
Buckley, T.R.1
Arensburger, P.2
Simon, C.3
Chambers, G.K.4
-
4
-
-
0036213207
-
The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support
-
BUCKLEY, T. R., AND C. W. CUNNINGHAM. 2002. The effects of nucleotide substitution model assumptions on estimates of nonparametric 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
-
5
-
-
0029096506
-
Sampling properties of DNA sequence data in phylogenetic analysis
-
CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol. Biol. Evol. 12:814-822.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 814-822
-
-
Cummings, M.P.1
Otto, S.P.2
Wakeley, J.3
-
6
-
-
0033153406
-
Genes and other samples of DNA sequence data for phylogenetic inference
-
CUMMINGS, M. P., S. P. OTTO, AND J. WAKELEY. 1999. Genes and other samples of DNA sequence data for phylogenetic inference. Biol. Bull. 196:345-350.
-
(1999)
Biol. Bull.
, vol.196
, pp. 345-350
-
-
Cummings, M.P.1
Otto, S.P.2
Wakeley, J.3
-
8
-
-
0037329108
-
Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability
-
DOUADY, C. J., F. DELSUC, Y. BOUCHER, W. F. DOOLITTLE, AND E. J. P. DOUZERY. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol. 20:248-254.
-
(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
-
-
0002344794
-
Bootstrapping methods: Another look at the jackknife
-
EFRON, B. 1979. Bootstrapping methods: Another look at the jackknife. Ann. Stat. 7:1-26.
-
(1979)
Ann. Stat.
, vol.7
, pp. 1-26
-
-
Efron, B.1
-
12
-
-
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. 27:401-410.
-
(1978)
Syst. Zool.
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
13
-
-
0000461280
-
Confidence intervals on phylogenies: An approach using the bootstrap
-
FELSENSTEIN, J. 1985. Confidence intervals on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
14
-
-
12044259827
-
Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull
-
FELSENSTEIN, J., AND H. KISHINO. 1993. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42:193-200.
-
(1993)
Syst. Biol.
, vol.42
, pp. 193-200
-
-
Felsenstein, J.1
Kishino, H.2
-
15
-
-
0002664746
-
Tests of significance in harmonic analysis
-
FISHER, R. A. 1929. Tests of significance in harmonic analysis. Proc. R. Soc. Lond. A 125:54-59.
-
(1929)
Proc. R. Soc. Lond. A
, vol.125
, pp. 54-59
-
-
Fisher, R.A.1
-
16
-
-
0026099641
-
Robustness of maximum likelihood tree estimation against different patterns of base substitutions
-
FUKAMI-KOBAYASHI, K., AND Y. TATENO. 1991. Robustness of maximum likelihood tree estimation against different patterns of base substitutions. J. Mol. Evol. 32:79-91.
-
(1991)
J. Mol. Evol.
, vol.32
, pp. 79-91
-
-
Fukami-Kobayashi, K.1
Tateno, Y.2
-
17
-
-
0028887457
-
Success of maximum likelihood phylogeny inference in the four-taxon case
-
GAUT, B. S., AND P. O. LEWIS. 1995. Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12:152-162.
-
(1995)
Mol. Biol. Evol.
, vol.12
, pp. 152-162
-
-
Gaut, B.S.1
Lewis, P.O.2
-
18
-
-
84972492387
-
Inference from iterative simulation using multiple sequences
-
GELMAN, A., AND D. B. RUBIN. 1992. Inference from iterative simulation using multiple sequences. Stat. Sci. 7:457-511.
-
(1992)
Stat. Sci.
, vol.7
, pp. 457-511
-
-
Gelman, A.1
Rubin, D.B.2
-
20
-
-
0026562079
-
The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies
-
HEDGES, S. B. 1992. The number of replications needed for accurate estimation of the bootstrap P value in phylogenetic studies. Mol. Biol. Evol. 9:366-369.
-
(1992)
Mol. Biol. Evol.
, vol.9
, pp. 366-369
-
-
Hedges, S.B.1
-
21
-
-
12044255023
-
Success of phylogenetic methods in the four-taxon case
-
HUELSENBECK, J. P., AND D. M. HILLIS. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42:247-264.
-
(1993)
Syst. Biol.
, vol.42
, pp. 247-264
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
22
-
-
0034849408
-
MrBayes: Bayesian inference of phylogenetic trees
-
HUELSENBECK, J. P., AND F. RONQUIST. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
23
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
HUELSENBECK, J. P., F. RONQUIST, R. NIELSEN, AND J. P. BOLLPACK. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollpack, J.P.4
-
24
-
-
0030305457
-
R: A language for data analysis and graphics
-
IHAKA, R., AND R. GENTLEMAN. 1996. R: A language for data analysis and graphics. J. Comput. Graph. Stat. 5:299-314.
-
(1996)
J. Comput. Graph. Stat.
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
25
-
-
0000732090
-
Evolution of protein molecules
-
(H. N. Munro, ed.). Academic Press, New York
-
JUKES, T. H., AND C. R. CANTOR. 1969. Evolution of protein molecules. Pages 21-132 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
26
-
-
0019296687
-
A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
-
KIMURA, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
-
(1980)
J. Mol. Evol.
, vol.16
, pp. 111-120
-
-
Kimura, M.1
-
27
-
-
0028177080
-
A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
-
KUHNER, M. K., AND J. FELSENSTEIN. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11:459-468.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 459-468
-
-
Kuhner, M.K.1
Felsenstein, J.2
-
28
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
LARGET, B., AND D. L. SIMON. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 750-759
-
-
Larget, B.1
Simon, D.L.2
-
29
-
-
0036005516
-
Molecular systematics of the eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood and Bayesian approaches
-
LEACHÉ, A. D., AND T. W. REEDER. 2002. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood and Bayesian approaches. Syst. Biol. 51:44-68.
-
(2002)
Syst. Biol.
, vol.51
, pp. 44-68
-
-
Leaché, A.D.1
Reeder, T.W.2
-
30
-
-
0035145155
-
Phylogenetic systematics turns over a new leaf
-
LEWIS, P. O. 2001. Phylogenetic systematics turns over a new leaf. Trends Ecol. Evol. 16:30-37.
-
(2001)
Trends Ecol. Evol.
, vol.16
, pp. 30-37
-
-
Lewis, P.O.1
-
32
-
-
0003814910
-
-
Distribution-free statistical methods, 2nd edition. Chapman & Hall, London
-
MARITZ, J. S. 1995. Distribution-free statistical methods, 2nd edition. Monographs on Statistics and Applied Probability 17. Chapman & Hall, London.
-
(1995)
Monographs on Statistics and Applied Probability
, vol.17
-
-
Maritz, J.S.1
-
33
-
-
0032906031
-
Bayesian phylogenetic inference via Markov chain Monte Carlo methods
-
MAU, B., M. NEWTON, AND B. LARGET. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55:1-12.
-
(1999)
Biometrics
, vol.55
, pp. 1-12
-
-
Mau, B.1
Newton, M.2
Larget, B.3
-
34
-
-
0042101429
-
Necessity is the mother of invention: A simple grid computing system using commodity tools
-
MYERS, D. S., AND M. P. CUMMINGS. 2003. Necessity is the mother of invention: A simple grid computing system using commodity tools. J. Parallel Distr. Com. 63:578-589.
-
(2003)
J. Parallel Distr. Com.
, vol.63
, pp. 578-589
-
-
Myers, D.S.1
Cummings, M.P.2
-
35
-
-
0001021240
-
Markov chain Monte Carlo for Bayesian analysis of evolutionary trees from aligned molecular sequences
-
NEWTON, M., B. MAU, AND B. LARGET. 1999. Markov chain Monte Carlo for Bayesian analysis of evolutionary trees from aligned molecular sequences. IMS Lecture Notes - Monograph Series 33:143-162.
-
(1999)
IMS Lecture Notes - Monograph Series
, vol.33
, pp. 143-162
-
-
Newton, M.1
Mau, B.2
Larget, B.3
-
36
-
-
0000353810
-
Inferring phylogenies from DNA sequence data: The effects of sampling
-
(P. H. Harvey, A. J. Leigh Brown, J. Maynard Smith, and S. Nee, eds.). Oxford Univ. Press, New York
-
OTTO, S. P., M. P. CUMMINGS, AND J. WAKELEY. 1996. Inferring phylogenies from DNA sequence data: The effects of sampling. Pages 103-115 in New uses for new phylogenies (P. H. Harvey, A. J. Leigh Brown, J. Maynard Smith, and S. Nee, eds.). Oxford Univ. Press, New York.
-
(1996)
New Uses for New Phylogenies
, pp. 103-115
-
-
Otto, S.P.1
Cummings, M.P.2
Wakeley, J.3
-
37
-
-
0029818407
-
Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
-
RANNALA, B., AND Z. YANG. 1996. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 43:304-311.
-
(1996)
J. Mol. Evol.
, vol.43
, pp. 304-311
-
-
Rannala, B.1
Yang, Z.2
-
38
-
-
0029526909
-
Objections to bootstrapping phylogenies: A critique
-
SANDERSON, M. J. 1995. Objections to bootstrapping phylogenies: A critique. Syst. Biol. 44:299-320.
-
(1995)
Syst. Biol.
, vol.44
, pp. 299-320
-
-
Sanderson, M.J.1
-
40
-
-
0037058983
-
Overcredibility of molecular phylogenetics obtained by Bayesian phylogenetics
-
SUZUKI, Y., G. V. GLAZKO, AND M. NEI. 2002. Overcredibility of molecular phylogenetics obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16138-16143
-
-
Suzuki, Y.1
Glazko, G.V.2
Nei, M.3
-
42
-
-
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
-
43
-
-
0027496790
-
Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA
-
WAKELEY, J. 1993. Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J. Mol. Evol. 37:613-623.
-
(1993)
J. Mol. Evol.
, vol.37
, pp. 613-623
-
-
Wakeley, J.1
-
44
-
-
0036368188
-
Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences
-
WHITTINGHAM, L. A., B. SLIKAS, D. W. WINKLER, AND F. H. SHELDON. 2002. Phylogeny of the tree swallow genus, Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences. Mol. Phylogenet. Evol. 22:430-441.
-
(2002)
Mol. Phylogenet. Evol.
, vol.22
, pp. 430-441
-
-
Whittingham, L.A.1
Slikas, B.2
Winkler, D.W.3
Sheldon, F.H.4
-
45
-
-
0036431235
-
Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
-
WILCOX, T. P., D. J. ZWICKL, T. A. HEATH, AND D. M. HILLIS. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371.
-
(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
-
46
-
-
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. 10:1369-1401.
-
(1993)
Mol. Biol. Evol.
, vol.10
, pp. 1369-1401
-
-
Yang, Z.1
-
47
-
-
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
-
48
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
YANG, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 15:555-556.
-
(1997)
Comput. Appl. Biosci.
, vol.15
, pp. 555-556
-
-
Yang, Z.1
-
49
-
-
0028267146
-
Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
-
YANG, Z., N. GOLDMAN, AND A. FRIDAY. 1994. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11:316-324.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 316-324
-
-
Yang, Z.1
Goldman, N.2
Friday, A.3
-
50
-
-
0030749810
-
Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
-
YANG, Z., AND B. RANNALA. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
-
(1997)
Mol. Biol. Evol.
, vol.14
, pp. 717-724
-
-
Yang, Z.1
Rannala, B.2
|