-
1
-
-
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. Lectures Math Life Sci (Amer Math Soc) 17: 57-86.
-
(1986)
Lectures Math Life Sci (Amer Math Soc)
, vol.17
, pp. 57-86
-
-
Tavaré, S.1
-
2
-
-
0000732090
-
Evolution of protein molecules
-
Munro HN, editor. New York: Academic Press
-
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN, editor. Mammalian protein metabolism. New York: Academic Press. pp. 21-123.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-123
-
-
Jukes, T.H.1
Cantor, C.R.2
-
3
-
-
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
-
4
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
DOI 10.1007/BF02101694
-
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174. (Pubitemid 16227864)
-
(1985)
Journal of Molecular Evolution
, vol.22
, Issue.2
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
5
-
-
0030451420
-
Among-site rate variation and its impact on phylogenetic analyses
-
Yang Z (1996) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol 11: 367-372.
-
(1996)
Trends Ecol Evol
, vol.11
, pp. 367-372
-
-
Yang, Z.1
-
6
-
-
0029844787
-
Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes
-
Simon C, Nigro L, Sullivan J, Holsinger K, Martin A, et al. (1996) Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes. Mol Biol Evol 13: 923-932. (Pubitemid 26284908)
-
(1996)
Molecular Biology and Evolution
, vol.13
, Issue.7
, pp. 923-932
-
-
Simon, C.1
Nigro, L.2
Sullivan, J.3
Holsinger, K.4
Martin, A.5
Grapputo, A.6
Franke, A.7
McIntosh, C.8
-
7
-
-
33845385936
-
Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA
-
DOI 10.1146/annurev.ecolsys.37.091305.110018
-
Simon C, Buckley TR, Frati F, Stewart JB, Beckenbach AT (2006) Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu Rev Ecol Evol Syst 37: 545-579. (Pubitemid 44907629)
-
(2006)
Annual Review of Ecology, Evolution, and Systematics
, vol.37
, pp. 545-579
-
-
Simon, C.1
Buckley, T.R.2
Frati, F.3
Stewart, J.B.4
Beckenbach, A.T.5
-
8
-
-
80054760378
-
Variation in the mutation rate across mammalian genomes
-
Hodgkinson A, Eyre-Walker A (2011) Variation in the mutation rate across mammalian genomes. Nat Rev Genet 12: 756-766.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 756-766
-
-
Hodgkinson, A.1
Eyre-Walker, A.2
-
9
-
-
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
-
10
-
-
0028205953
-
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
-
Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site. Mol Biol Evol 11: 261-277. (Pubitemid 24075751)
-
(1994)
Molecular Biology and Evolution
, vol.11
, Issue.2
, pp. 261-277
-
-
Tateno, Y.1
Takezaki, N.2
Nei, M.3
-
11
-
-
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 GK (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.K.3
-
12
-
-
0035527373
-
Should we use model-based methods for phylogenetic inference when we know that 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 that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst Biol 50: 723-729.
-
(2001)
Syst Biol
, vol.50
, pp. 723-729
-
-
Sullivan, J.1
Swofford, D.L.2
-
13
-
-
84867750911
-
The influence of rate heterogeneity among sites on the time dependence of molecular rates
-
Soubrier J, Steel M, Lee MSY, Sarkissian CD, Guindon S, et al. (2012) The influence of rate heterogeneity among sites on the time dependence of molecular rates. Mol Biol Evol 29: 3345-3358.
-
(2012)
Mol Biol Evol
, vol.29
, pp. 3345-3358
-
-
Soubrier, J.1
Steel, M.2
Lee, M.S.Y.3
Sarkissian, C.D.4
Guindon, S.5
-
14
-
-
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
-
15
-
-
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
-
16
-
-
0033913138
-
DNA evidence for morphological and cryptic cenozoic speciations in the Anaspididae, 'living fossils' from the triassic
-
DOI 10.1046/j.1420-9101.2000.00207.x
-
Jarman SN, Elliott NG (2000) DNA evidence for morphological and cryptic Cenozoic speciations in the Anaspididae, 'living fossils' from the Triassic. J Evol Biol 13: 624-633. (Pubitemid 30466915)
-
(2000)
Journal of Evolutionary Biology
, vol.13
, Issue.4
, pp. 624-633
-
-
Jarman, S.N.1
Elliott, N.G.2
-
17
-
-
66749153836
-
Correcting for purifying selection: An improved human mitochondrial molecular clock
-
Soares P, Ermini L, Thomson N, Mormina M, Rito T, et al. (2009) Correcting for purifying selection: an improved human mitochondrial molecular clock. Am J Hum Genet 84: 740-759.
-
(2009)
Am J Hum Genet
, vol.84
, pp. 740-759
-
-
Soares, P.1
Ermini, L.2
Thomson, N.3
Mormina, M.4
Rito, T.5
-
18
-
-
84871167089
-
Arrival of Paleo-Indians to the southern cone of South America: New clues from mitogenomes
-
de St Pierre M, Gandini F, Perego UA, Bodner M, Gomez-Carballa A, et al. (2012) Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes. PLOS ONE 7.
-
(2012)
PLOS ONE
, pp. 7
-
-
De St Pierre, M.1
Gandini, F.2
Perego, U.A.3
Bodner, M.4
Gomez-Carballa, A.5
-
19
-
-
27544508958
-
A Gamma mixture model better accounts for among site rate heterogeneity
-
Mayrose I, Friedman N, Pupko T (2005) A Gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics 21: 151-158.
-
(2005)
Bioinformatics
, vol.21
, pp. 151-158
-
-
Mayrose, I.1
Friedman, N.2
Pupko, T.3
-
20
-
-
0014092973
-
A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome C as a model case
-
Fitch WM, Margoliash E (1967) A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome C as a model case. Biochem Genet 1: 65-71.
-
(1967)
Biochem Genet
, vol.1
, pp. 65-71
-
-
Fitch, W.M.1
Margoliash, E.2
-
21
-
-
0022502392
-
An estimation of the number of invariable sites is necessary for the accurate estimation of the number of nucleotide substitutions since a common ancestor
-
Gershowitz H, Rucknagel DL, Tashian RE, editors. New York: Alan R. Liss, Inc.
-
Fitch WM (1986) An estimation of the number of invariable sites is necessary for the accurate estimation of the number of nucleotide substitutions since a common ancestor. In: Gershowitz H, Rucknagel DL, Tashian RE, editors. Evolutionary perspectives and the new genetics. New York: Alan R. Liss, Inc. pp. 149-159.
-
(1986)
Evolutionary Perspectives and the New Genetics
, pp. 149-159
-
-
Fitch, W.M.1
-
22
-
-
0024359678
-
Rates of molecular evolution and the fraction of nucleotide positions free to vary
-
Palumbi SR (1989) Rates of molecular evolution and the fraction of nucleotide positions free to vary. J Mol Evol 29: 180-187.
-
(1989)
J Mol Evol
, vol.29
, pp. 180-187
-
-
Palumbi, S.R.1
-
23
-
-
0024661142
-
Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated
-
Shoemaker JS, Fitch WM (1989) Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol Biol Evol 6: 270-289.
-
(1989)
Mol Biol Evol
, vol.6
, pp. 270-289
-
-
Shoemaker, J.S.1
Fitch, W.M.2
-
24
-
-
0031046929
-
Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony
-
Tourasse NJ, Gouy M (1997) Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Mol Biol Evol 14: 287-298. (Pubitemid 27102674)
-
(1997)
Molecular Biology and Evolution
, vol.14
, Issue.3
, pp. 287-298
-
-
Tourasse, N.J.1
Gouy, M.2
-
25
-
-
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: 546-557.
-
(1995)
Mol Biol Evol
, vol.12
, pp. 546-557
-
-
Gu, X.1
Fu, Y.X.2
Li, W.H.3
-
26
-
-
0031297695
-
General Time-Reversible Distances with Unequal Rates across Sites: Mixing gamma and Inverse Gaussian Distributions with Invariant Sites
-
DOI 10.1006/mpev.1997.0452, PII S1055790397904528
-
Waddell PJ, Steel MA (1997) General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites. Mol Phylogenet Evol 8: 398-414. (Pubitemid 127347898)
-
(1997)
Molecular Phylogenetics and Evolution
, vol.8
, Issue.3
, pp. 398-414
-
-
Waddell, P.J.1
Steel, M.A.2
-
27
-
-
0016355478
-
A new look at the statistical model identification
-
Akaike H (1981) A new look at the statistical model identification. IEEE Trans Autom Control: 716-723.
-
(1981)
IEEE Trans Autom Control
, pp. 716-723
-
-
Akaike, H.1
-
28
-
-
0000120766
-
Estimating the dimension of a model
-
Schwartz G (1978) Estimating the dimension of a model. Ann Stat 6: 461-464.
-
(1978)
Ann Stat
, vol.6
, pp. 461-464
-
-
Schwartz, G.1
-
29
-
-
77955290199
-
Performance of criteria for selecting evolutionary models in phylogenetics: A comprehensive study based on simulated datasets
-
Luo A, Qiao HJ, Zhang YZ, Shi WF, Ho SYW, et al. (2010) Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets. BMC Evol Biol 10.
-
(2010)
BMC Evol Biol
, pp. 10
-
-
Luo, A.1
Qiao, H.J.2
Zhang, Y.Z.3
Shi, W.F.4
Ho, S.Y.W.5
-
30
-
-
33645816587
-
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
-
Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6: 29.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 29
-
-
Keane, T.M.1
Creevey, C.J.2
Pentony, M.M.3
Naughton, T.J.4
Mclnerney, J.O.5
-
31
-
-
33846047594
-
Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila
-
DOI 10.1038/nature05388, PII NATURE05388
-
Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, et al. (2007) Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature 445: 82-85. (Pubitemid 46067305)
-
(2007)
Nature
, vol.445
, Issue.7123
, pp. 82-85
-
-
Haag-Liautard, C.1
Dorris, M.2
Maside, X.3
Macaskill, S.4
Halligan, D.L.5
Charlesworth, B.6
Keightley, P.D.7
-
32
-
-
84876823246
-
Mutation load: The fitness of individuals in populations where deleterious alleles are abundant
-
Agrawal AF, Whitlock MC (2012) Mutation load: the fitness of individuals in populations where deleterious alleles are abundant. Annu Rev Ecol Evol Syst 43: 115-135.
-
(2012)
Annu Rev Ecol Evol Syst
, vol.43
, pp. 115-135
-
-
Agrawal, A.F.1
Whitlock, M.C.2
-
34
-
-
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: 1347-1356. (Pubitemid 29473229)
-
(1999)
Molecular Biology and Evolution
, vol.16
, Issue.10
, pp. 1347-1356
-
-
Sullivan, J.1
Swofford, D.L.2
Naylor, G.J.P.3
-
35
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
39
-
-
0036804625
-
Mapping mutations on phylogenies
-
Nielsen R (2002) Mapping mutations on phylogenies. Syst Biol 51: 729-739.
-
(2002)
Syst Biol
, vol.51
, pp. 729-739
-
-
Nielsen, R.1
-
40
-
-
33645029984
-
SIMMAP: Stochastic character mapping of discrete traits on phylogenies
-
Bollback JP (2006) SIMMAP: stochastic character mapping of discrete traits on phylogenies. BMC Bioinformatics 7: 88.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 88
-
-
Bollback, J.P.1
-
41
-
-
57749178865
-
Hantavirus evolution in relation to its rodent and insectivore hosts: No evidence for codivergence
-
Ramsden C, Holmes EC, Charleston MA (2009) Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence. Mol Biol Evol 26: 143-153.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 143-153
-
-
Ramsden, C.1
Holmes, E.C.2
Charleston, M.A.3
-
42
-
-
79955457408
-
Bayesian estimation of substitution rates from ancient DNA sequences with low information content
-
Ho SYW, Lanfear R, Phillips MJ, Barnes I, Thomas JA, et al. (2011) Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Syst Biol 60: 366-374.
-
(2011)
Syst Biol
, vol.60
, pp. 366-374
-
-
Ho, S.Y.W.1
Lanfear, R.2
Phillips, M.J.3
Barnes, I.4
Thomas, J.A.5
-
43
-
-
80053525593
-
Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins
-
Kumar S, Bellis C, Zlojutro M, Melton PE, Blangero J, et al. (2011) Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins. BMC Evol Biol 11: 293.
-
(2011)
BMC Evol Biol
, vol.11
, pp. 293
-
-
Kumar, S.1
Bellis, C.2
Zlojutro, M.3
Melton, P.E.4
Blangero, J.5
-
44
-
-
77949718257
-
FastTree 2 - approximately maximum-likelihood trees for large alignments
-
Price MN, Dehal PS, Arkin AP (2010) FastTree 2 - approximately maximum-likelihood trees for large alignments. PLOS ONE 5: e9490.
-
(2010)
PLOS ONE
, vol.5
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
45
-
-
31344433677
-
An empirical examination of the utility of codon-substitution models in phylogeny reconstruction
-
DOI 10.1080/10635150500354688
-
Ren F, Tanaka H, Yang Z (2005) An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Syst Biol 54: 808-818. (Pubitemid 43142296)
-
(2005)
Systematic Biology
, vol.54
, Issue.5
, pp. 808-818
-
-
Ren, F.1
Tanaka, H.2
Yang, Z.3
-
46
-
-
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: 447-455.
-
(2001)
J Mol Evol
, vol.53
, pp. 447-455
-
-
Felsenstein, J.1
-
47
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
DOI 10.1093/bioinformatics/bti191
-
Stamatakis A, Ludwig T, Meier H (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21: 456-463. (Pubitemid 40310232)
-
(2005)
Bioinformatics
, vol.21
, Issue.4
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
49
-
-
84873603201
-
Bayesian selection of nucleotide substitution models and their site assignments
-
Wu CH, Suchard MA, Drummond AJ (2013) Bayesian selection of nucleotide substitution models and their site assignments. Mol Biol Evol 30: 669-688.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 669-688
-
-
Wu, C.H.1
Suchard, M.A.2
Drummond, A.J.3
-
50
-
-
0034619822
-
Mitochondrial genome variation and the origin of modem humans
-
DOI 10.1038/35047064
-
Ingman M, Kaessmann H, Paabo S, Gyllensten U (2000) Mitochondrial genome variation and the origin of modern humans. Nature 408: 708-713. (Pubitemid 32015984)
-
(2000)
Nature
, vol.408
, Issue.6813
, pp. 708-713
-
-
Ingman, M.1
Kaessmann, H.2
Paabo, S.3
Gyllensten, U.4
-
51
-
-
84877780848
-
Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans
-
Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, et al. (2013) Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans. Nat Commun 4: 1764.
-
(2013)
Nat Commun
, vol.4
, pp. 1764
-
-
Brotherton, P.1
Haak, W.2
Templeton, J.3
Brandt, G.4
Soubrier, J.5
-
52
-
-
84876151646
-
A revised timescale for human evolution based on ancient mitochondrial genomes
-
Fu QM, Mittnik A, Johnson PLF, Bos K, Lari M, et al. (2013) A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol 23: 553-559.
-
(2013)
Curr Biol
, vol.23
, pp. 553-559
-
-
Fu, Q.M.1
Mittnik, A.2
Johnson, P.L.F.3
Bos, K.4
Lari, M.5
-
54
-
-
53349127137
-
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
-
Worobey M, Gemmel M, Teuwen DE, Haselkorn T, Kunstman K, et al. (2008) Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 455: 661-664.
-
(2008)
Nature
, vol.455
, pp. 661-664
-
-
Worobey, M.1
Gemmel, M.2
Teuwen, D.E.3
Haselkorn, T.4
Kunstman, K.5
|