-
1
-
-
0002367729
-
MOLPHY v. 2.3: Programs for molecular phylogenetics based on maximum likelihood
-
Adachi, J. & Hasegawa, M. 1996 MOLPHY v. 2.3: programs for molecular phylogenetics based on maximum likelihood. Comput. Sci. Monogr. 28, 1-150.
-
(1996)
Comput. Sci. Monogr
, vol.28
, pp. 1-150
-
-
Adachi, J.1
Hasegawa, M.2
-
2
-
-
0033920569
-
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
-
Adachi, J., Waddell, P., Martin, W. & Hasegawa, M. 2000 Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol. 50, 348-358.
-
(2000)
J. Mol. Evol
, vol.50
, pp. 348-358
-
-
Adachi, J.1
Waddell, P.2
Martin, W.3
Hasegawa, M.4
-
3
-
-
0000708831
-
Mixtures of Dirichlet processes with applications to non-parametric problems
-
Antoniak, C. E. 1974 Mixtures of Dirichlet processes with applications to non-parametric problems. Ann. Stat. 2, 1152-1174.
-
(1974)
Ann. Stat
, vol.2
, pp. 1152-1174
-
-
Antoniak, C.E.1
-
4
-
-
0039998729
-
Exponential numbers
-
Bell, E. T. 1934 Exponential numbers. Am. Math. Monthly 41, 411-419.
-
(1934)
Am. Math. Monthly
, vol.41
, pp. 411-419
-
-
Bell, E.T.1
-
5
-
-
0005723678
-
Tetrapod relationships: The molecular evidence
-
ed. C. Patterson, pp, Cambridge, UK: Cambridge University Press
-
Bishop, M. J. & Friday, A. E. 1987 Tetrapod relationships: the molecular evidence. In Molecules and morphology in evolution: conflict or compromise? (ed. C. Patterson), pp. 123-140. Cambridge, UK: Cambridge University Press.
-
(1987)
Molecules and morphology in evolution: Conflict or compromise
, pp. 123-140
-
-
Bishop, M.J.1
Friday, A.E.2
-
6
-
-
0035089952
-
Phylogenetic relationships, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae)
-
Bollback, J. & Huelsenbeck, J. P. 2001 Phylogenetic relationships, genome evolution, and host specificity of single-stranded RNA bacteriophage (Family Leviviridae). J. Mol. Evol. 52, 117-128.
-
(2001)
J. Mol. Evol
, vol.52
, pp. 117-128
-
-
Bollback, J.1
Huelsenbeck, J.P.2
-
7
-
-
0031694349
-
Conflict amongst individual mitochondrial proteins in resolving the phylogeny of eutherian orders
-
Cao, Y., Janke, A., Waddell, P. J., Westerman, M., Takenaka, O., Murata, S., Okada, N., Pääbo, S. & Hasegawa, M. 1998 Conflict amongst individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47, 307-322.
-
(1998)
J. Mol. Evol
, vol.47
, pp. 307-322
-
-
Cao, Y.1
Janke, A.2
Waddell, P.J.3
Westerman, M.4
Takenaka, O.5
Murata, S.6
Okada, N.7
Pääbo, S.8
Hasegawa, M.9
-
8
-
-
0022422660
-
Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations 1984
-
Cornish-Bowden, A. 1985 Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 13, 3021-3030.
-
(1985)
Nucleic Acids Res
, vol.13
, pp. 3021-3030
-
-
Cornish-Bowden, A.1
-
9
-
-
0000228203
-
A model of evolutionary change in proteins
-
Washington, DC: National Biomedical Research Foundation
-
Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. 1978 A model of evolutionary change in proteins. In: Atlas of protein sequence and structure, vol. 5, Supplement 3, pp. 345-352. Washington, DC: National Biomedical Research Foundation.
-
(1978)
Atlas of protein sequence and structure
, vol.5
, Issue.SUPPL.EMENT 3
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
10
-
-
0036017382
-
RArtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
-
Dimmic, M. W., Rest, J. S., Mindell, D. P. & Goldstein, D. 2002 RArtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J. Mol. Evol. 55, 65-73.
-
(2002)
J. Mol. Evol
, vol.55
, pp. 65-73
-
-
Dimmic, M.W.1
Rest, J.S.2
Mindell, D.P.3
Goldstein, D.4
-
11
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein, J. 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376.
-
(1981)
J. Mol. Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
12
-
-
0001120413
-
A Bayesian analysis of some non-parametric problems
-
Ferguson, T. S. 1973 A Bayesian analysis of some non-parametric problems. Ann. Stat. 1, 209-230.
-
(1973)
Ann. Stat
, vol.1
, pp. 209-230
-
-
Ferguson, T.S.1
-
13
-
-
0030750055
-
Long term trends in the evolution of H(3) HA1 human influenza type A
-
Fitch, W. M., Bush, R. M., Bender, C. A. & Cox, N. J. 1997 Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl Acad. Sci. USA 94, 7712-7718.
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 7712-7718
-
-
Fitch, W.M.1
Bush, R.M.2
Bender, C.A.3
Cox, N.J.4
-
14
-
-
0001582213
-
Inference and monitoring convergence
-
eds W. R. Gilks, S. Richardson & D. J. Spiegelhalter, pp, London, UK: Chapman and Hall
-
Gelman, A. 1996 Inference and monitoring convergence. In Markov Chain Monte Carlo in practice (eds W. R. Gilks, S. Richardson & D. J. Spiegelhalter), pp. 131-143. London, UK: Chapman and Hall.
-
(1996)
Markov Chain Monte Carlo in practice
, pp. 131-143
-
-
Gelman, A.1
-
15
-
-
84972492387
-
Inferences from iterative simulation using multiple sequences
-
Gelman, A. & Rubin, D. B. 1992 Inferences 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
-
16
-
-
0037118191
-
Partition-distance: A problem and class of perfect graphs arising in clustering
-
Gusfield, D. 2002 Partition-distance: a problem and class of perfect graphs arising in clustering. Inf. Process. Lett. 82, 159-164.
-
(2002)
Inf. Process. Lett
, vol.82
, pp. 159-164
-
-
Gusfield, D.1
-
17
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
Hastings, W. K. 1970 Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57, 97-109.
-
(1970)
Biometrika
, vol.57
, pp. 97-109
-
-
Hastings, W.K.1
-
18
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
Henikoff, S. & Henikoff, J. G. 1992 Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA 89, 10 915-10 919.
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
-
-
Henikoff, S.1
Henikoff, J.G.2
-
19
-
-
34249066206
-
Inference of population structure under a Dirichlet process model
-
Huelsenbeck, J. P. & Andolfatto, P. 2007 Inference of population structure under a Dirichlet process model. Genetics 175, 1787-1802.
-
(2007)
Genetics
, vol.175
, pp. 1787-1802
-
-
Huelsenbeck, J.P.1
Andolfatto, P.2
-
20
-
-
0035861456
-
Bayesian inference of phylogeny and its impact on evolutionary biology
-
Huelsenbeck, J. P., Ronquist, F., Nielsen, R. & Bollback, J. 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
Bollback, J.4
-
21
-
-
2442671519
-
Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
-
Huelsenbeck, J. P., Larget, B. & Alfaro, M. E. 2004 Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol. 21, 1123-1133.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1123-1133
-
-
Huelsenbeck, J.P.1
Larget, B.2
Alfaro, M.E.3
-
22
-
-
33646586721
-
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences
-
Huelsenbeck, J. P., Jain, S., Frost, S. W. D. & Pond, S. L. K. 2006 A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc. Natl Acad. Sci. USA 103, 6263-6268.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 6263-6268
-
-
Huelsenbeck, J.P.1
Jain, S.2
Frost, S.W.D.3
Pond, S.L.K.4
-
23
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D. T., Taylor, W. R. & Thornton, J. M. 1992 The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
-
(1992)
Comput. Appl. Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
24
-
-
0000732090
-
Evolution of protein molecules
-
ed. H. N. Munro, pp, New York, NY: Academic Press
-
Jukes, T. H. & Cantor, C. R. 1969 Evolution of protein molecules. In Mammalian protein metabolism (ed. H. N. Munro), pp. 21-123. New York, NY: Academic Press.
-
(1969)
Mammalian protein metabolism
, pp. 21-123
-
-
Jukes, T.H.1
Cantor, C.R.2
-
25
-
-
0019296687
-
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
-
Kimura, M. 1980 A simple method for estimating evolutionary rates 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
-
26
-
-
34547675965
-
An empirical codon model for protein sequence evolution
-
Kosiol, C., Holmes, I. & Goldman, N. 2007 An empirical codon model for protein sequence evolution. Mol. Biol. Evol. 24, 1464-1479.
-
(2007)
Mol. Biol. Evol
, vol.24
, pp. 1464-1479
-
-
Kosiol, C.1
Holmes, I.2
Goldman, N.3
-
28
-
-
0032976397
-
Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
-
Larget, B. & Simon, D. L. 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
-
-
2442691520
-
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
-
Lartillot, N. & Philippe, H. 2004 A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095-1109.
-
(2004)
Mol. Biol. Evol
, vol.21
, pp. 1095-1109
-
-
Lartillot, N.1
Philippe, H.2
-
30
-
-
0033460110
-
Bayes factors: What they are and what they are not
-
Lavine, M. & Schervish, M. J. 1999 Bayes factors: what they are and what they are not. Am. Stat. 53, 119-122.
-
(1999)
Am. Stat
, vol.53
, pp. 119-122
-
-
Lavine, M.1
Schervish, M.J.2
-
31
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. 1953 Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 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
-
32
-
-
0034922289
-
Modeling amino acid replacement
-
Muller, T. & Vingron, M. 2000 Modeling amino acid replacement. J. Comput. Biol. 7, 761-776.
-
(2000)
J. Comput. Biol
, vol.7
, pp. 761-776
-
-
Muller, T.1
Vingron, M.2
-
33
-
-
77950032550
-
Markov chain sampling methods for Dirichlet process mixture models
-
Neal, R. M. 2000 Markov chain sampling methods for Dirichlet process mixture models. J. Comput. Graph. Stat. 9, 249-265.
-
(2000)
J. Comput. Graph. Stat
, vol.9
, pp. 249-265
-
-
Neal, R.M.1
-
34
-
-
85020814905
-
-
Rambaut, A. & Drummond, A. J. 2007 TRACER v. 1.4. See http://beast.bio.ed.ac.uk/Tracer.
-
Rambaut, A. & Drummond, A. J. 2007 TRACER v. 1.4. See http://beast.bio.ed.ac.uk/Tracer.
-
-
-
-
35
-
-
0041386108
-
MRBAYES 3: Bayesian phylogenetic inference under mixed models
-
Ronquist, F. & Huelsenbeck, J. P. 2003 MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
36
-
-
37349019755
-
-
Smith, B. J. 2007 boa: an R package for MCMC output convergence assessment and posterior inference. J. Stat. Softw. 21, 1-37.
-
Smith, B. J. 2007 boa: an R package for MCMC output convergence assessment and posterior inference. J. Stat. Softw. 21, 1-37.
-
-
-
-
38
-
-
85020767605
-
-
Swofford, D. L. 1998 PAUP*: phylogenetic analysis using parsimony (*and other methods), v. 4.0.b10. Sunderland, MA: Sinauer Associates, Inc.
-
Swofford, D. L. 1998 PAUP*: phylogenetic analysis using parsimony (*and other methods), v. 4.0.b10. Sunderland, MA: Sinauer Associates, Inc.
-
-
-
-
39
-
-
0027157960
-
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
-
Tamura, K. & Nei, M. 1993 Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
-
(1993)
Mol. Biol. Evol
, vol.10
, pp. 512-526
-
-
Tamura, K.1
Nei, M.2
-
40
-
-
0002671410
-
Some probabilistic and statistical problems on the analysis of DNA sequences
-
Tavaré, S. 1986 Some probabilistic and statistical problems on 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
-
41
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein familes using a maximum likelihood approach
-
Whelan, S. & Goldman, N. 2001 A general empirical model of protein evolution derived from multiple protein familes using a maximum likelihood approach. Mol. Biol. Evol. 18, 691-699.
-
(2001)
Mol. Biol. Evol
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
42
-
-
0041385962
-
Pandit: A database of protein and associated nucleotide domains with inferred trees
-
Whelan, S., de Bakker, P. & Goldman, N. 2003 Pandit: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics 19, 1556-1563.
-
(2003)
Bioinformatics
, vol.19
, pp. 1556-1563
-
-
Whelan, S.1
de Bakker, P.2
Goldman, N.3
-
43
-
-
33644878388
-
PANDIT: An evolution-centric database of protein and associated nucleotide domains with inferred trees
-
Whelan, S., de Bakker, P., Quevillon, E., Rodriguez, N. & Goldman, N. 2006 PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res. 34, D327-D331.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Whelan, S.1
de Bakker, P.2
Quevillon, E.3
Rodriguez, N.4
Goldman, N.5
-
44
-
-
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
-
45
-
-
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
-
46
-
-
0031792828
-
Models of amino acid substitution and applications to mitochondrial protein evolution
-
Yang, Z., Nielsen, R. & Hasegawa, M. 1998 Models of amino acid substitution and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15, 1600-1611.
-
(1998)
Mol. Biol. Evol
, vol.15
, pp. 1600-1611
-
-
Yang, Z.1
Nielsen, R.2
Hasegawa, M.3
-
47
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure
-
Yang, Z., Nielsen, R., Goldman, N. & Pedersen, A. M. K. 2000 Codon-substitution models for heterogeneous selection pressure. Genetics 155, 431-449.
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.K.4
-
48
-
-
0009650916
-
Population dynamics of flaviviruses revealed by molecular phylogenies
-
Zanotto, P. M., Gould, E. A., Gao, G. F., Harvey, P. H. & Holmes, E. C. 1996 Population dynamics of flaviviruses revealed by molecular phylogenies. Proc. Natl Acad. Sci. USA 93, 548-553.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 548-553
-
-
Zanotto, P.M.1
Gould, E.A.2
Gao, G.F.3
Harvey, P.H.4
Holmes, E.C.5
-
49
-
-
12444337674
-
Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics
-
Zwickl, D. J. & Holder, M. T. 2004 Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst. Biol. 53, 877-888.
-
(2004)
Syst. Biol
, vol.53
, pp. 877-888
-
-
Zwickl, D.J.1
Holder, M.T.2
|