-
1
-
-
18744382506
-
ProtTest: Selection of best-fit models of protein evolution
-
Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105
-
(2005)
Bioinformatics
, vol.21
, pp. 2104-2105
-
-
Abascal, F.1
Zardoya, R.2
Posada, D.3
-
2
-
-
14544289241
-
Accounting for uncertainty in the tree topology has little effect on the decision-theory approach to model selection in phylogeny estimation
-
Abdo Z, Minin VN, Joyce P, Sullivan J (2005) Accounting for uncertainty in the tree topology has little effect on the decision-theory 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.N.2
Joyce, P.3
Sullivan, J.4
-
3
-
-
0002367729
-
MOLPHY version 2.3: Programs for molecular phylogenetics based in maximum likelihood
-
Adachi J, Hasegawa M (1996) MOLPHY version 2.3: programs for molecular phylogenetics based in maximum likelihood. Comput Sci Monogr 28:1-150
-
(1996)
Comput Sci Monogr
, vol.28
, pp. 1-150
-
-
Adachi, J.1
Hasegawa, M.2
-
4
-
-
0033920569
-
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
-
Adachi J, Waddell PJ, 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.J.2
Martin, W.3
Hasegawa, M.4
-
5
-
-
0037329391
-
Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
-
Alfaro ME, Zoller S, Lutzoni F (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
-
6
-
-
0034897709
-
Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
-
Anisimova M, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18, 1585-1592
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1585-1592
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
7
-
-
0036272936
-
Accuracy and power of Bayes prediction of amino acid sites under positive selection
-
Anisimova M, Bielawski JP, Yang Z (2002) Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol Biol Evol 19:950-958
-
(2002)
Mol Biol Evol
, vol.19
, pp. 950-958
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
8
-
-
0042208362
-
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
-
Anisimova M, Nielsen R, Yang Z (2003) Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236
-
(2003)
Genetics
, vol.164
, pp. 1229-1236
-
-
Anisimova, M.1
Nielsen, R.2
Yang, Z.3
-
9
-
-
0036804729
-
Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny
-
Aris-Brosou S, Yang Z (2002) Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst Biol 51:703-714
-
(2002)
Syst Biol
, vol.51
, pp. 703-714
-
-
Aris-Brosou, S.1
Yang, Z.2
-
10
-
-
0032900678
-
Median-joining networks for inferring intraspecific phylogenies
-
Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 16:37-48
-
(1999)
Mol Biol Evol
, vol.16
, pp. 37-48
-
-
Bandelt, H.J.1
Forster, P.2
Rohl, A.3
-
11
-
-
3042842589
-
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
-
Bielawski JP, Yang Z (2004) A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol 59:121-132
-
(2004)
J Mol Evol
, vol.59
, pp. 121-132
-
-
Bielawski, J.P.1
Yang, Z.2
-
12
-
-
0036790011
-
Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference
-
Brauer MJ, Holder MT, Dries LA, Zwickl DJ, Lewis PO, Hillis DM (2002) Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference. Mol Biol Evol 19:1717-1726
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1717-1726
-
-
Brauer, M.J.1
Holder, M.T.2
Dries, L.A.3
Zwickl, D.J.4
Lewis, P.O.5
Hillis, D.M.6
-
13
-
-
0000367652
-
The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
-
Bremer K (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803
-
(1988)
Evolution
, vol.42
, pp. 795-803
-
-
Bremer, K.1
-
14
-
-
0000131403
-
Cross-validation methods
-
Browne M (2000) Cross-validation methods. J Math Psychol 44:108-132
-
(2000)
J Math Psychol
, vol.44
, pp. 108-132
-
-
Browne, M.1
-
15
-
-
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 16:564-566
-
(1999)
Mol Biol Evol
, vol.16
, pp. 564-566
-
-
Bruno, W.J.1
Halpern, A.L.2
-
16
-
-
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 51:509-523
-
(2002)
Syst Biol
, vol.51
, pp. 509-523
-
-
Buckley, T.R.1
-
17
-
-
0036213207
-
The effects of nucleotide substitution model assumptions on estimates of nonparametric bootstrap support
-
Buckley TR, Cunningham CW (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
-
19
-
-
0031694349
-
Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders
-
Cao Y, Janke A, Waddell PJ, Westerman M, Takenaka O, Murata S, Okada N, Paabo S, Hasegawa M (1998) Conflict among 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
Paabo, S.8
Hasegawa, M.9
-
20
-
-
33644911496
-
Recombination estimation under complex evolutionary models with the coalescent composite likelihood method
-
Carvajal-Rodríguez A, Crandall KA, Posada D (2006) Recombination estimation under complex evolutionary models with the coalescent composite likelihood method. Mol Biol Evol 13:817-827
-
(2006)
Mol Biol Evol
, vol.13
, pp. 817-827
-
-
Carvajal-Rodríguez, A.1
Crandall, K.A.2
Posada, D.3
-
21
-
-
22844440900
-
Evaluating intraspecific "network" construction methods using simulated sequence data: Do existing algorithms outperform the global maximum parsimony approach?
-
Cassens I, Mardulyn P, Milinkovitch MC (2005) Evaluating intraspecific "network" construction methods using simulated sequence data: do existing algorithms outperform the global maximum parsimony approach? Syst Biol 54:363-372
-
(2005)
Syst Biol
, vol.54
, pp. 363-372
-
-
Cassens, I.1
Mardulyn, P.2
Milinkovitch, M.C.3
-
22
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540-552
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
23
-
-
0033771358
-
TCS: A computer program to estimate gene genealogies
-
Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657-1659
-
(2000)
Mol Ecol
, vol.9
, pp. 1657-1659
-
-
Clement, M.1
Posada, D.2
Crandall, K.A.3
-
24
-
-
0030032992
-
Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences
-
Crandall KA (1996) Multiple interspecies transmissions of human and simian T-cell leukemia/lymphoma virus type I sequences. Mol Biol Evol 13:115-131
-
(1996)
Mol Biol Evol
, vol.13
, pp. 115-131
-
-
Crandall, K.A.1
-
25
-
-
0033028201
-
Parallel evolution of drug resistance in HIV: Failure of nonsynonymous/synonymous substitution rate ratio to detect selection
-
Crandall KA, Kelsey CR, Imamichi H, Lane HC, Salzman NP (1999) Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol Biol Evol 16:372-382
-
(1999)
Mol Biol Evol
, vol.16
, pp. 372-382
-
-
Crandall, K.A.1
Kelsey, C.R.2
Imamichi, H.3
Lane, H.C.4
Salzman, N.P.5
-
26
-
-
33744908932
-
Phylogenomics and molecular evolution of polyomaviruses
-
Ahsan N ed, Landes BioScience, Georgetown
-
Crandall KA, Pérez-Losada M, Christensen RG, McClellan DA, Viscidi RP (2005) Phylogenomics and molecular evolution of polyomaviruses. In: Ahsan N (ed) Polyomavirus and human diseases. Landes BioScience, Georgetown, pp 1-14
-
(2005)
Polyomavirus and Human Diseases
, pp. 1-14
-
-
Crandall, K.A.1
Pérez-Losada, M.2
Christensen, R.G.3
McClellan, D.A.4
Viscidi, R.P.5
-
27
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff MO ed, National Biomedical Research Foundation, Washington
-
Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure. National Biomedical Research Foundation, Washington, pp 345-352
-
(1978)
Atlas of Protein Sequence and Structure
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
28
-
-
0036943052
-
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle
-
Desper R, Gascuel O (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol 9:687-705
-
(2002)
J Comput Biol
, vol.9
, pp. 687-705
-
-
Desper, R.1
Gascuel, O.2
-
29
-
-
0036017382
-
RtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
-
Dimmic MW, Rest JS, Mindell DP, Goldstein RA (2002) rtREV: 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, R.A.4
-
30
-
-
0035164634
-
Multilocus sequence typing system for Campylobacter jejuni
-
Dingle KE, Colles FM, Wareing DR, Ure R, Fox AJ, Bolton FE, Bootsma HJ, Willems RJ, Urwin R, Maiden MC (2001) Multilocus sequence typing system for Campylobacter jejuni. J Clin Microbiol 39:14-23
-
(2001)
J Clin Microbiol
, vol.39
, pp. 14-23
-
-
Dingle, K.E.1
Colles, F.M.2
Wareing, D.R.3
Ure, R.4
Fox, A.J.5
Bolton, F.E.6
Bootsma, H.J.7
Willems, R.J.8
Urwin, R.9
Maiden, M.C.10
-
32
-
-
0037329108
-
Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability
-
Douady CJ, Delsuc F, Boucher Y, Doolittle WF, Douzery EJ (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.5
-
33
-
-
0036021407
-
Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
-
Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320
-
(2002)
Genetics
, vol.161
, pp. 1307-1320
-
-
Drummond, A.J.1
Nicholls, G.K.2
Rodrigo, A.G.3
Solomon, W.4
-
35
-
-
17744381574
-
Bayesian coalescent inference of past population dynamics from molecular sequences
-
Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol 22:1185-1192
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1185-1192
-
-
Drummond, A.J.1
Rambaut, A.2
Shapiro, B.3
Pybus, O.G.4
-
36
-
-
0003234370
-
Multiple alignment for structural, functional, or phylogenetic analyses of homologous sequences
-
Higgins D, Taylor W eds, Oxford University Press, Oxford
-
Duret L, Abdeddaim S (2000) Multiple alignment for structural, functional, or phylogenetic analyses of homologous sequences. In: Higgins D, Taylor W (eds) Bioinformatics, sequence, structure and databanks. Oxford University Press, Oxford, pp 155-167
-
(2000)
Bioinformatics, Sequence, Structure and Databanks
, pp. 155-167
-
-
Duret, L.1
Abdeddaim, S.2
-
37
-
-
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
-
38
-
-
0035576346
-
Revealing the demographic histories of species using DNA sequences
-
Emerson BC, Paradis E, Thébaud C (2001) Revealing the demographic histories of species using DNA sequences. Trends Ecol Evol 16:707-716
-
(2001)
Trends Ecol Evol
, vol.16
, pp. 707-716
-
-
Emerson, B.C.1
Paradis, E.2
Thébaud, C.3
-
39
-
-
0033018649
-
Gene genealogies in geographically structured populations
-
Epperson BK (1999) Gene genealogies in geographically structured populations. Genetics 152:797-806
-
(1999)
Genetics
, vol.152
, pp. 797-806
-
-
Epperson, B.K.1
-
40
-
-
0028069723
-
Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: Molecular variance parsimony
-
Excoffier L, Smouse PE (1994) Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136:343-359
-
(1994)
Genetics
, vol.136
, pp. 343-359
-
-
Excoffier, L.1
Smouse, P.E.2
-
41
-
-
0037423837
-
Traces of human migrations in Helicobacter pylori populations
-
Falush D, Wirth T, Linz B, Pritchard JK, Stephens M, Kidd M, Blaser MJ, Graham DY, Vacher S, Pérez-Pérez GI, Yamaoka Y, Megraud F, Otto K, Reichard U, Katzowitsch E, Wang X, Achtman M, Suerbaum S (2003) Traces of human migrations in Helicobacter pylori populations. Science 299:1582-1585
-
(2003)
Science
, vol.299
, pp. 1582-1585
-
-
Falush, D.1
Wirth, T.2
Linz, B.3
Pritchard, J.K.4
Stephens, M.5
Kidd, M.6
Blaser, M.J.7
Graham, D.Y.8
Vacher, S.9
Pérez-Pérez, G.I.10
Yamaoka, Y.11
Megraud, F.12
Otto, K.13
Reichard, U.14
Katzowitsch, E.15
Wang, X.16
Achtman, M.17
Suerbaum, S.18
-
42
-
-
0035675042
-
Estimating recombination rates from population genetic data
-
Fearnhead P, Donnelly P (2001) Estimating recombination rates from population genetic data. Genetics 159:1299-1318
-
(2001)
Genetics
, vol.159
, pp. 1299-1318
-
-
Fearnhead, P.1
Donnelly, P.2
-
43
-
-
0034128665
-
Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data
-
Feil EJ, Smith JM, Enright MC, Spratt BG (2000) Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:1439-1450
-
(2000)
Genetics
, vol.154
, pp. 1439-1450
-
-
Feil, E.J.1
Smith, J.M.2
Enright, M.C.3
Spratt, B.G.4
-
44
-
-
0037853350
-
How clonal is Staphylococcus aureus?
-
Feil EJ, Cooper JE, Grundmann H, Robinson DA, Enright MC, Berendt T, Peacock SJ, Smith JM, Murphy M, Spratt BG, Moore CE, Day NP (2003) How clonal is Staphylococcus aureus? J Bacteriol 185:3307-3316
-
(2003)
J Bacteriol
, vol.185
, pp. 3307-3316
-
-
Feil, E.J.1
Cooper, J.E.2
Grundmann, H.3
Robinson, D.A.4
Enright, M.C.5
Berendt, T.6
Peacock, S.J.7
Smith, J.M.8
Murphy, M.9
Spratt, B.G.10
Moore, C.E.11
Day, N.P.12
-
45
-
-
84959798530
-
Cases in which parsimony or compatibility methods will be positively misleading
-
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410
-
(1978)
Syst Zool
, vol.27
, pp. 401-410
-
-
Felsenstein, J.1
-
46
-
-
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
-
47
-
-
0000461280
-
Confidence limits on phylogenies: An approach using the bootstrap
-
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
-
(1985)
Evolution
, vol.39
, pp. 783-791
-
-
Felsenstein, J.1
-
50
-
-
0035057075
-
Molecular evolution of transferrin: Evidence for positive selection in salmonids
-
Ford MJ (2001) Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol Biol Evol 18:639-647
-
(2001)
Mol Biol Evol
, vol.18
, pp. 639-647
-
-
Ford, M.J.1
-
51
-
-
0042573997
-
A codon-based model of host-specific selection in parasites, with an application to the influenza A virus
-
Forsberg R, Christiansen FB (2003) A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol Biol Evol 20:1252-1259
-
(2003)
Mol Biol Evol
, vol.20
, pp. 1252-1259
-
-
Forsberg, R.1
Christiansen, F.B.2
-
53
-
-
0027220656
-
Maximum likelihood estimation of population parameters
-
Fu YX, Li WH (1993) Maximum likelihood estimation of population parameters. Genetics 134:1261-1270
-
(1993)
Genetics
, vol.134
, pp. 1261-1270
-
-
Fu, Y.X.1
Li, W.H.2
-
54
-
-
0027616543
-
Alignment-ambiguous nucleotide sites and the exclusion of systematic data
-
Gatesy J, De Salle R, Wheeler W (1993) Alignment-ambiguous nucleotide sites and the exclusion of systematic data. Mol Phylogenet Evol 2:152-157
-
(1993)
Mol Phylogenet Evol
, vol.2
, pp. 152-157
-
-
Gatesy, J.1
De Salle, R.2
Wheeler, W.3
-
55
-
-
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 12:152-162
-
(1995)
Mol Biol Evol
, vol.12
, pp. 152-162
-
-
Gaut, B.S.1
Lewis, P.O.2
-
56
-
-
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 11:725-736
-
(1994)
Mol Biol Evol
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
57
-
-
1642554676
-
Reading the entrails of chickens: Molecular timescales of evolution and the illusion of precision
-
Graur D, Martin W (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends Genet 20:80-86
-
(2004)
Trends Genet
, vol.20
, pp. 80-86
-
-
Graur, D.1
Martin, W.2
-
58
-
-
77956889087
-
Reversible jump Markov chain Monte Carlo computation and Bayesian model determination
-
Green PJ (1995) Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732
-
(1995)
Biometrika
, vol.82
, pp. 711-732
-
-
Green, P.J.1
-
59
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phyhlogenies by maximum likelihood
-
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phyhlogenies by maximum likelihood. Syst Biol 52:696-704
-
(2003)
Syst Biol
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.2
-
61
-
-
0020286044
-
Branch and bound algorithms to determine minimal evolutionary trees
-
Hendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Math Biosci 59:277-290
-
(1982)
Math Biosci
, vol.59
, pp. 277-290
-
-
Hendy, M.D.1
Penny, D.2
-
62
-
-
0026458378
-
Amino acid substitution matrices for protein blocks
-
Henikoff S, Henikoff JG (1992) Amino acid substitution matrices for protein blocks. Proc Natl Acad Sci USA 89:10915-10919
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
63
-
-
3142714474
-
Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis
-
Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760
-
(2004)
Genetics
, vol.167
, pp. 747-760
-
-
Hey, J.1
Nielsen, R.2
-
64
-
-
12044253190
-
An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
-
Hillis DM, Bull JJ (1993) An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol 42:182-192
-
(1993)
Syst Biol
, vol.42
, pp. 182-192
-
-
Hillis, D.M.1
Bull, J.J.2
-
65
-
-
0001935493
-
Gene genealogies and the coalescent process
-
Futuyma D, Antonovics J eds, Oxford University Press, New York
-
Hudson RR (1991) Gene genealogies and the coalescent process. In: Futuyma D, Antonovics J (eds) Oxford surveys in evolutionary biology, vol 7. Oxford University Press, New York, pp 1-44
-
(1991)
Oxford Surveys in Evolutionary Biology
, vol.7
, pp. 1-44
-
-
Hudson, R.R.1
-
66
-
-
0035692320
-
Two-locus sampling distributions and their application
-
Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159:1805-1817
-
(2001)
Genetics
, vol.159
, pp. 1805-1817
-
-
Hudson, R.R.1
-
67
-
-
11944268967
-
Performance of phylogenetic methods in simulation
-
Huelsenbeck JP (1995) Performance of phylogenetic methods in simulation. Syst Biol 44:17-48
-
(1995)
Syst Biol
, vol.44
, pp. 17-48
-
-
Huelsenbeck, J.P.1
-
68
-
-
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 28:437-466
-
(1997)
Annu Rev Ecol Syst
, vol.28
, pp. 437-466
-
-
Huelsenbeck, J.P.1
Crandall, K.A.2
-
69
-
-
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 42:247-264
-
(1993)
Syst Biol
, vol.42
, pp. 247-264
-
-
Huelsenbeck, J.P.1
Hillis, D.M.2
-
70
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogeny
-
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
71
-
-
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 294:2310-2314
-
(2001)
Science
, vol.294
, pp. 2310-2314
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
Nielsen, R.3
Bollback, J.P.4
-
72
-
-
0036806280
-
Potential applications and pitfalls of Bayesian inference of phylogeny
-
Huelsenbeck JP, Larget B, Miller RE, Ronquist F (2002) Potential applications and pitfalls of Bayesian inference of phylogeny. Syst Biol 51:673-688
-
(2002)
Syst Biol
, vol.51
, pp. 673-688
-
-
Huelsenbeck, J.P.1
Larget, B.2
Miller, R.E.3
Ronquist, F.4
-
73
-
-
2442671519
-
Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo
-
Huelsenbeck JP, Larget B, Alfaro ME (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
-
74
-
-
2442612820
-
Distances that perfectly mislead
-
Huson DH, Steel M (2004) Distances that perfectly mislead. Syst Biol 53:327-332
-
(2004)
Syst Biol
, vol.53
, pp. 327-332
-
-
Huson, D.H.1
Steel, M.2
-
75
-
-
0035002725
-
Efficiency of parallel direct optimization
-
Janies DA, Wheeler WC (2001) Efficiency of parallel direct optimization. Cladistics 17:S71-S82
-
(2001)
Cladistics
, vol.17
-
-
Janies, D.A.1
Wheeler, W.C.2
-
77
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM (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
-
78
-
-
0000732090
-
Evolution of protein molecules
-
Munro HM ed, Academic, New York
-
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HM (ed) Mammalian protein metabolism. Academic, New York, pp 21-132
-
(1969)
Mammalian Protein Metabolism
, pp. 21-132
-
-
Jukes, T.H.1
Cantor, C.R.2
-
79
-
-
84950934893
-
Bayes factors and model uncertainty
-
Kass RE, Raftery AE (1995) Bayes factors and model uncertainty. J Am Stat Assoc 90:773-775
-
(1995)
J Am Stat Assoc
, vol.90
, pp. 773-775
-
-
Kass, R.E.1
Raftery, A.E.2
-
80
-
-
0034819230
-
Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny
-
Katoh K, Kuma K, Miyata T (2001) Genetic algorithm-based maximum-likelihood analysis for molecular phylogeny. J Mol Evol 53:477-484
-
(2001)
J Mol Evol
, vol.53
, pp. 477-484
-
-
Katoh, K.1
Kuma, K.2
Miyata, T.3
-
81
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33:511-518
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
82
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059-3066
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
84
-
-
0024307824
-
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea
-
Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170-179
-
(1989)
J Mol Evol
, vol.29
, pp. 170-179
-
-
Kishino, H.1
Hasegawa, M.2
-
86
-
-
0031835126
-
Maximum likelihood estimation of population growth rates based on the coalescent
-
Kuhner MK, Yamato J, Felsenstein J (1998) Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149:429-434
-
(1998)
Genetics
, vol.149
, pp. 429-434
-
-
Kuhner, M.K.1
Yamato, J.2
Felsenstein, J.3
-
87
-
-
33644993800
-
-
University of Washington
-
Kuhner MK, Yamato J, Beerli P, Smith LP, Rynes E, Walkup E, Li C, Sloan J, Colacurcio P, Felsenstein J (2005) LAMARC version 2.0.2. University of Washington
-
(2005)
LAMARC Version 2.0.2
-
-
Kuhner, M.K.1
Yamato, J.2
Beerli, P.3
Smith, L.P.4
Rynes, E.5
Walkup, E.6
Li, C.7
Sloan, J.8
Colacurcio, P.9
Felsenstein, J.10
-
88
-
-
3242810318
-
MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment
-
Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150-163
-
(2004)
Brief Bioinform
, vol.5
, pp. 150-163
-
-
Kumar, S.1
Tamura, K.2
Nei, M.3
-
89
-
-
0036005516
-
Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches
-
Leaché AD, Reeder TW (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
-
90
-
-
0036679128
-
The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
-
Lemmon AR, Milinkovitch MC (2002) The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation. Proc Natl Acad Sci USA 99:10516-10521
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 10516-10521
-
-
Lemmon, A.R.1
Milinkovitch, M.C.2
-
91
-
-
0031892789
-
A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data
-
Lewis PO (1998) A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol Biol Evol 15, 277-283
-
(1998)
Mol Biol Evol
, vol.15
, pp. 277-283
-
-
Lewis, P.O.1
-
93
-
-
0041886963
-
A hidden Markov model for progressive multiple alignment
-
Löytynoja A, Milinkovitch MC (2003) A hidden Markov model for progressive multiple alignment. Bioinformatics 19:1505-1513
-
(2003)
Bioinformatics
, vol.19
, pp. 1505-1513
-
-
Löytynoja, A.1
Milinkovitch, M.C.2
-
94
-
-
25444443637
-
Bayesian coestimation of phylogeny and sequence alignment
-
Lunter G, Miklos I, Drummond A, Jensen JL, Hein J (2005) Bayesian coestimation of phylogeny and sequence alignment. BMC Bioinformatics 6:83
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 83
-
-
Lunter, G.1
Miklos, I.2
Drummond, A.3
Jensen, J.L.4
Hein, J.5
-
95
-
-
0034351388
-
Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology
-
Lutzoni F, Wagner P, Reeb V, Zoller S (2000) Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Syst Biol 49:628-651
-
(2000)
Syst Biol
, vol.49
, pp. 628-651
-
-
Lutzoni, F.1
Wagner, P.2
Reeb, V.3
Zoller, S.4
-
97
-
-
0029075130
-
Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase
-
Mansky LM, Temin HM (1995) Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J Virol 69:5087-5094
-
(1995)
J Virol
, vol.69
, pp. 5087-5094
-
-
Mansky, L.M.1
Temin, H.M.2
-
98
-
-
0030309199
-
Protein phylogenetic inference using maximum likelihood with a genetic algorithm
-
Matsuda H (1996) Protein phylogenetic inference using maximum likelihood with a genetic algorithm. Paper presented at the Pacific symposium on biocomputing
-
(1996)
The Pacific Symposium on Biocomputing
-
-
Matsuda, H.1
-
99
-
-
0001931821
-
Do bacteria have population genetics?
-
Baumberg JP ed, Press Syndicate of the University of Cambridge, Cambridge
-
Maynard Smith J (1995) Do bacteria have population genetics? In: Baumberg JP (ed) Population genetics of bacteria. Press Syndicate of the University of Cambridge, Cambridge, pp 1-12
-
(1995)
Population Genetics of Bacteria
, pp. 1-12
-
-
Maynard Smith, J.1
-
100
-
-
0034982702
-
Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains
-
McClellan DA, McCracken KG (2001) Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol Biol Evol 18:917-925
-
(2001)
Mol Biol Evol
, vol.18
, pp. 917-925
-
-
McClellan, D.A.1
McCracken, K.G.2
-
101
-
-
14544300682
-
Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins
-
McClellan DA, Palfreyman EJ, Smith MJ, Moss JL, Christensen RG, Sailsbery JK (2005) Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. Mol Biol Evol 22:437-455
-
(2005)
Mol Biol Evol
, vol.22
, pp. 437-455
-
-
McClellan, D.A.1
Palfreyman, E.J.2
Smith, M.J.3
Moss, J.L.4
Christensen, R.G.5
Sailsbery, J.K.6
-
102
-
-
0036199914
-
A coalescent-based method for detecting and estimating recombination from gene sequences
-
McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231-1241
-
(2002)
Genetics
, vol.160
, pp. 1231-1241
-
-
McVean, G.1
Awadalla, P.2
Fearnhead, P.3
-
103
-
-
0035157374
-
Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila
-
McVean GAT, Vieira J (2001) Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 157:245-257
-
(2001)
Genetics
, vol.157
, pp. 245-257
-
-
McVean, G.A.T.1
Vieira, J.2
-
104
-
-
12444303202
-
Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing
-
Meats E, Feil EJ, Stringer S, Cody AJ, Goldstein R, Kroll JS, Popovic T, Spratt BG (2003) Characterization of encapsulated and noncapsulated Haemophilus influenzae and determination of phylogenetic relationships by multilocus sequence typing. J Clin Microbiol 41:1623-1636
-
(2003)
J Clin Microbiol
, vol.41
, pp. 1623-1636
-
-
Meats, E.1
Feil, E.J.2
Stringer, S.3
Cody, A.J.4
Goldstein, R.5
Kroll, J.S.6
Popovic, T.7
Spratt, B.G.8
-
105
-
-
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 52:674-683
-
(2003)
Syst Biol
, vol.52
, pp. 674-683
-
-
Minin, V.1
Abdo, Z.2
Joyce, P.3
Sullivan, J.4
-
106
-
-
0019134329
-
Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application
-
Miyata T, Yasunaga T (1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J Mol Evol 16:23-36
-
(1980)
J Mol Evol
, vol.16
, pp. 23-36
-
-
Miyata, T.1
Yasunaga, T.2
-
107
-
-
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
-
108
-
-
0022507362
-
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
-
Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418-426
-
(1986)
Mol Biol Evol
, vol.3
, pp. 418-426
-
-
Nei, M.1
Gojobori, T.2
-
109
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.2
-
110
-
-
0033504552
-
The parsimony ratchet, a new method for rapid parsimony analyses
-
Nixon KC (1999) The parsimony ratchet, a new method for rapid parsimony analyses. Cladistics 15:407-414
-
(1999)
Cladistics
, vol.15
, pp. 407-414
-
-
Nixon, K.C.1
-
111
-
-
0000913208
-
Coalescent theory
-
Balding D, Bishop M, Cannings C eds, Wiley, Chichester
-
Nordborg M (2001) Coalescent theory. In: Balding D, Bishop M, Cannings C (eds) Handbook of statistical genetics. Wiley, Chichester, pp 179-212
-
(2001)
Handbook of Statistical Genetics
, pp. 179-212
-
-
Nordborg, M.1
-
112
-
-
0036208872
-
Recent progress in multiple sequence alignment: A survey
-
Notredame C (2002) Recent progress in multiple sequence alignment: a survey. Pharmacogenetics 3:131-144
-
(2002)
Pharmacogenetics
, vol.3
, pp. 131-144
-
-
Notredame, C.1
-
113
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, Heringa J (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 302:205-217
-
(2000)
J Mol Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
115
-
-
34447277667
-
Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*
-
Ogden TH, Rosenberg MS (2007) Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*. Syst Biol 56:182-193
-
(2007)
Syst Biol
, vol.56
, pp. 182-193
-
-
Ogden, T.H.1
Rosenberg, M.S.2
-
116
-
-
2942619012
-
3DCoffee: Combining protein sequences and structures within multiple sequence alignments
-
O'Sullivan O, Suhre K, Abergel C, Higgins DG, Notredame C (2004) 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol 340:385-395
-
(2004)
J Mol Biol
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
118
-
-
4243140058
-
A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence of character-state data
-
Pagel M, Meade A (2004) A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence of character-state data. Syst Biol 53:571-581
-
(2004)
Syst Biol
, vol.53
, pp. 571-581
-
-
Pagel, M.1
Meade, A.2
-
119
-
-
1642410112
-
Beyond Fst: Analysis of population genetic data for conservation
-
Pearse DE, Crandall KA (2004) Beyond Fst: analysis of population genetic data for conservation. Conserv Genet 5:585-602
-
(2004)
Conserv Genet
, vol.5
, pp. 585-602
-
-
Pearse, D.E.1
Crandall, K.A.2
-
120
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
121
-
-
0001596085
-
The role of models in reconstructing evolutionary trees
-
Scotland RW, Siebert DJ, Williams DM eds, Clarendon, Oxford
-
Penny D, Lockhart PJ, Steel MA, Hendy MD (1994) The role of models in reconstructing evolutionary trees. In: Scotland RW, Siebert DJ, Williams DM (eds) Models in phylogenetic reconstruction. Clarendon, Oxford, pp 211-230
-
(1994)
Models in Phylogenetic Reconstruction
, pp. 211-230
-
-
Penny, D.1
Lockhart, P.J.2
Steel, M.A.3
Hendy, M.D.4
-
122
-
-
23944506345
-
Population genetics of Neisseria gonorrhoeae in a high prevalence community using a hyper-variable outer membrane porB and thirteen slowly-evolving housekeeping genes
-
Pérez-Losada M, Viscidi RP, Demma JC, Zenilman J, Crandall KA (2005) Population genetics of Neisseria gonorrhoeae in a high prevalence community using a hyper-variable outer membrane porB and thirteen slowly-evolving housekeeping genes. Mol Biol Evol 22:1887-1902
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1887-1902
-
-
Pérez-Losada, M.1
Viscidi, R.P.2
Demma, J.C.3
Zenilman, J.4
Crandall, K.A.5
-
123
-
-
33344458092
-
Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data
-
Pérez-Losada M, Browne EB, Madsen A, Wirth T, Viscidi RP, Crandall KA (2006) Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infect Genet Evol 6:97-112
-
(2006)
Infect Genet Evol
, vol.6
, pp. 97-112
-
-
Pérez-Losada, M.1
Browne, E.B.2
Madsen, A.3
Wirth, T.4
Viscidi, R.P.5
Crandall, K.A.6
-
124
-
-
14544275616
-
A genetic algorithm approach to detecting lineage-specific variation in selection pressure
-
Pond SL, Frost SD (2005) A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol 22:478-485
-
(2005)
Mol Biol Evol
, vol.22
, pp. 478-485
-
-
Pond, S.L.1
Frost, S.D.2
-
125
-
-
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
-
126
-
-
0031773680
-
MODELTEST: Testing the model of DNA substitution
-
Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
127
-
-
0035923699
-
Evaluation of methods for detecting recombination from DNA sequences: Computer simulations
-
Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA 98:13757-13762
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 13757-13762
-
-
Posada, D.1
Crandall, K.A.2
-
128
-
-
0036183042
-
The effect of recombination on the accuracy of phylogeny estimation
-
Posada D, Crandall KA (2002) The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol 54:396-402
-
(2002)
J Mol Evol
, vol.54
, pp. 396-402
-
-
Posada, D.1
Crandall, K.A.2
-
129
-
-
0034100234
-
GeoDis: A program for the cladistic nested analysis of the geographical distribution of genetic haplotypes
-
Posada D, Crandall KA, Templeton AR (2000) GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Mol Ecol 9:487-488
-
(2000)
Mol Ecol
, vol.9
, pp. 487-488
-
-
Posada, D.1
Crandall, K.A.2
Templeton, A.R.3
-
131
-
-
0036900111
-
Combining multiple data sets in a likelihood analysis: Which models are the best?
-
Pupko T, Huchon D, Cao Y, Okada N, Hasegawa M (2002) Combining multiple data sets in a likelihood analysis: Which models are the best? Mol Biol Evol 19:2294-2307
-
(2002)
Mol Biol Evol
, vol.19
, pp. 2294-2307
-
-
Pupko, T.1
Huchon, D.2
Cao, Y.3
Okada, N.4
Hasegawa, M.5
-
132
-
-
0036773016
-
GENIE: Estimating demographic history from molecular phylogenies
-
Pybus OG, Rambaut A (2002) GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18:1404-1405
-
(2002)
Bioinformatics
, vol.18
, pp. 1404-1405
-
-
Pybus, O.G.1
Rambaut, A.2
-
133
-
-
0000783674
-
Hypothesis testing and model selection
-
Gilks WR, Richardson S, Spiegelhalter DJ eds, Chapman & Hall, London
-
Raftery AE (1996) Hypothesis testing and model selection. In: Gilks WR, Richardson S, Spiegelhalter DJ (eds) Markov chain Monte Carlo in practice. Chapman & Hall, London, pp 163-188
-
(1996)
Markov Chain Monte Carlo in Practice
, pp. 163-188
-
-
Raftery, A.E.1
-
135
-
-
22844450838
-
Joint Bayesian estimation of alignment and phylogeny
-
Redelings BD, Suchard MA (2005) Joint Bayesian estimation of alignment and phylogeny. Syst Biol 54:401-418
-
(2005)
Syst Biol
, vol.54
, pp. 401-418
-
-
Redelings, B.D.1
Suchard, M.A.2
-
136
-
-
4544313053
-
The ring of life provides evidence for a genome fusion origin of eukaryotes
-
Rivera MC, Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152-155
-
(2004)
Nature
, vol.431
, pp. 152-155
-
-
Rivera, M.C.1
Lake, J.A.2
-
137
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP (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
-
138
-
-
25444528241
-
Evolutionary distance estimation and fidelity of pair wise sequence alignment
-
Rosenberg MS (2005) Evolutionary distance estimation and fidelity of pair wise sequence alignment. BMC Bioinformatics 6:102
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 102
-
-
Rosenberg, M.S.1
-
139
-
-
0027185401
-
Theoretical foundation of the minimum-evolution method of phylogenetic inference
-
Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073-1095
-
(1993)
Mol Biol Evol
, vol.10
, pp. 1073-1095
-
-
Rzhetsky, A.1
Nei, M.2
-
140
-
-
18844420035
-
Detecting sitespecific physicochemical selective pressures: Applications to the class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system
-
Sainudiin R, Wong WS, Yogeeswaran K, Nasrallah JB, Yang Z, Nielsen R (2005) Detecting sitespecific physicochemical selective pressures: applications to the class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J Mol Evol 60:315-326
-
(2005)
J Mol Evol
, vol.60
, pp. 315-326
-
-
Sainudiin, R.1
Wong, W.S.2
Yogeeswaran, K.3
Nasrallah, J.B.4
Yang, Z.5
Nielsen, R.6
-
141
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
142
-
-
0029526909
-
Objections to bootstrapping phylogenies: A critique
-
Sanderson MJ (1995) Objections to bootstrapping phylogenies: a critique. Syst Biol 44:299-320
-
(1995)
Syst Biol
, vol.44
, pp. 299-320
-
-
Sanderson, M.J.1
-
143
-
-
0034351392
-
Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae)
-
Sanderson MJ, Wojciechowski MF (2000) Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae). Syst Biol 49:671-685
-
(2000)
Syst Biol
, vol.49
, pp. 671-685
-
-
Sanderson, M.J.1
Wojciechowski, M.F.2
-
144
-
-
0033793521
-
Consequences of recombination on traditional phylogenetic analysis
-
Schierup MH, Hein J (2000) Consequences of recombination on traditional phylogenetic analysis. Genetics 156:879-891
-
(2000)
Genetics
, vol.156
, pp. 879-891
-
-
Schierup, M.H.1
Hein, J.2
-
145
-
-
0036205377
-
TREE-PUZZLE: Maximumlikelihood phylogenetic analysis using quartets and parallel computing
-
Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximumlikelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504
-
(2002)
Bioinformatics
, vol.18
, pp. 502-504
-
-
Schmidt, H.A.1
Strimmer, K.2
Vingron, M.3
Von Haeseler, A.4
-
147
-
-
0000120766
-
Estimating the dimensions of a model
-
Schwarz G (1978) Estimating the dimensions of a model. Ann Stat 6:461-464
-
(1978)
Ann Stat
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
148
-
-
0036623258
-
An approximately unbiased test of phylogenetic tree selection
-
Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492-508
-
(2002)
Syst Biol
, vol.51
, pp. 492-508
-
-
Shimodaira, H.1
-
149
-
-
0032766857
-
Multiple comparisons of log-likelihoods with applications to phylogenetic inference
-
Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114-1116
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1114-1116
-
-
Shimodaira, H.1
Hasegawa, M.2
-
150
-
-
0036139287
-
CONSEL: For assessing the confidence of phylogenetic tree selection
-
Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247
-
(2001)
Bioinformatics
, vol.17
, pp. 1246-1247
-
-
Shimodaira, H.1
Hasegawa, M.2
-
151
-
-
0037986694
-
Potential impact of recombination on sitewise approaches for detecting positive natural selection
-
Shriner D, Nickle DC, Jensen MA, Mullins JI (2003) Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet Res 81:115-121
-
(2003)
Genet Res
, vol.81
, pp. 115-121
-
-
Shriner, D.1
Nickle, D.C.2
Jensen, M.A.3
Mullins, J.I.4
-
152
-
-
67649345185
-
An improved Bonferroni procedure for multiple tests of significance
-
Simes RJ (1986) An improved Bonferroni procedure for multiple tests of significance. Biometrika 73:751-754
-
(1986)
Biometrika
, vol.73
, pp. 751-754
-
-
Simes, R.J.1
-
154
-
-
35448939728
-
Molecular phylogenetics for conservation biology
-
Purvis A, Brooks T, Gittleman J ed, Cambridge University Press, Cambridge
-
Sinclair EA, Pérez-Losada M, Crandall K. A (2005) Molecular phylogenetics for conservation biology. In: Purvis A, Brooks T, Gittleman J (ed) Phylogeny and conservation. Cambridge University Press, Cambridge, pp 19-56
-
(2005)
Phylogeny and Conservation
, pp. 19-56
-
-
Sinclair, E.A.1
Pérez-Losada, M.2
Crandall, K.A.3
-
156
-
-
14644397888
-
RAxML-III: A fast program for maximum likelihoodbased inference of large phylogenetic trees
-
Stamatakis AT, Ludwig H, Meier H (2005) RAxML-III: a fast program for maximum likelihoodbased inference of large phylogenetic trees. Bioinformatics 21:456-463
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.T.1
Ludwig, H.2
Meier, H.3
-
157
-
-
0002242481
-
Inference under the coalescent
-
Balding DJ, Cannings C, Bishop M eds, Wiley, Chichester
-
Stephens M (2001) Inference under the coalescent. In: Balding DJ, Cannings C, Bishop M (eds) Handbook of statistical genetics. Wiley, Chichester, pp 213-238
-
(2001)
Handbook of Statistical Genetics
, pp. 213-238
-
-
Stephens, M.1
-
158
-
-
0035211479
-
Exploring the demographic history of DNA sequences using the generalized skyline plot
-
Strimmer K, Pybus OG (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol 18:2298-2305
-
(2001)
Mol Biol Evol
, vol.18
, pp. 2298-2305
-
-
Strimmer, K.1
Pybus, O.G.2
-
159
-
-
41049111540
-
Inferring confidence sets of possibly misspecified gene trees
-
Strimmer K, Rambaut A (2002) Inferring confidence sets of possibly misspecified gene trees. Proc Biol Sci 269:137-142
-
(2002)
Proc Biol Sci
, vol.269
, pp. 137-142
-
-
Strimmer, K.1
Rambaut, A.2
-
160
-
-
0034983646
-
Bayesian selection of continuous-time Markov chain evolutionary models
-
Suchard MA, Weiss RE, Sinsheimer JS (2001) Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 18:1001-1013
-
(2001)
Mol Biol Evol
, vol.18
, pp. 1001-1013
-
-
Suchard, M.A.1
Weiss, R.E.2
Sinsheimer, J.S.3
-
161
-
-
0002618746
-
Are guinea pigs rodents? The importance of adequate models in molecular phylogenies
-
Sullivan J, Swofford DL (1997) Are guinea pigs rodents? The importance of adequate models in molecular phylogenies. J Mamm Evol 4:77-86
-
(1997)
J Mamm Evol
, vol.4
, pp. 77-86
-
-
Sullivan, J.1
Swofford, D.L.2
-
163
-
-
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 46:426-440
-
(1997)
Syst Biol
, vol.46
, pp. 426-440
-
-
Sullivan, J.1
Markert, J.A.2
Kilpatrick, C.W.3
-
164
-
-
0032849322
-
A method for detecting positive selection at single amino acid sites
-
Suzuki Y, Gojobori T (1999) A method for detecting positive selection at single amino acid sites. Mol Biol Evol 16:1315-1328
-
(1999)
Mol Biol Evol
, vol.16
, pp. 1315-1328
-
-
Suzuki, Y.1
Gojobori, T.2
-
165
-
-
0034904729
-
ADAPTSITE: Detecting natural selection at single amino acid sites
-
Suzuki Y, Gojobori T, Nei M (2001) ADAPTSITE: detecting natural selection at single amino acid sites. Bioinformatics 17:660-661
-
(2001)
Bioinformatics
, vol.17
, pp. 660-661
-
-
Suzuki, Y.1
Gojobori, T.2
Nei, M.3
-
166
-
-
0037058983
-
Overcredibililty of molecular phylogenies obtained by Bayesian phylogenetics
-
Suzuki Y, Glazko GV, Nei M (2002) Overcredibililty of molecular phylogenies 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
-
168
-
-
0001336205
-
Phylogenetic inference
-
Hillis DM, Moritz C, Mable BK eds, Sinauer, Sunderland
-
Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinauer, Sunderland, pp 407-514
-
(1996)
Molecular Systematics
, pp. 407-514
-
-
Swofford, D.L.1
Olsen, G.J.2
Waddell, P.J.3
Hillis, D.M.4
-
169
-
-
3342920601
-
Prospects for inferring very large phylogenies by using the neighbor-joining method
-
Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA 101:11030-11035
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 11030-11035
-
-
Tamura, K.1
Nei, M.2
Kumar, S.3
-
170
-
-
17744373692
-
Characterization of the long-wavelength opsin from Mecoptera and Siphonaptera: Does a flea see?
-
Taylor SD, de la Cruz KD, Porter ML, Whiting MF (2005) Characterization of the long-wavelength opsin from Mecoptera and Siphonaptera: does a flea see? Mol Biol Evol 22:1165-1174
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1165-1174
-
-
Taylor, S.D.1
De La Cruz, K.D.2
Porter, M.L.3
Whiting, M.F.4
-
171
-
-
0032055149
-
Nested clade analyses of phylogeographic data: Testing hypotheses about gene flow and population history
-
Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol Ecol 7:381-397
-
(1998)
Mol Ecol
, vol.7
, pp. 381-397
-
-
Templeton, A.R.1
-
172
-
-
1642339467
-
Statistical phylogeography: Methods of evaluating and minimizing inference errors
-
Templeton AR (2004) Statistical phylogeography: methods of evaluating and minimizing inference errors. Mol Ecol 13:789-810
-
(2004)
Mol Ecol
, vol.13
, pp. 789-810
-
-
Templeton, A.R.1
-
173
-
-
0026662698
-
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation
-
Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619-633
-
(1992)
Genetics
, vol.132
, pp. 619-633
-
-
Templeton, A.R.1
Crandall, K.A.2
Sing, C.F.3
-
174
-
-
0027278852
-
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination
-
Templeton AR, Sing CF (1993) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134:659-669
-
(1993)
Genetics
, vol.134
, pp. 659-669
-
-
Templeton, A.R.1
Sing, C.F.2
-
175
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
176
-
-
0031574072
-
The CLUSTAL-X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
177
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
Thompson JD, Plewniak F, Poch O (1999a) BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15:87-88
-
(1999)
Bioinformatics
, vol.15
, pp. 87-88
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
178
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson JD, Plewniak F, Poch O (1999b) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27:2682-2690
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
179
-
-
27844555472
-
Bridging the gap between molecular epidemiologists and evolutionists
-
Tibayrenc M (2005) Bridging the gap between molecular epidemiologists and evolutionists. Trends Microbiol 13:575-580
-
(2005)
Trends Microbiol
, vol.13
, pp. 575-580
-
-
Tibayrenc, M.1
-
180
-
-
0000576595
-
Markov-chains for exploring posterior distributions
-
Tierney L (1994) Markov-chains for exploring posterior distributions. Ann Stat 22:1701-1728
-
(1994)
Ann Stat
, vol.22
, pp. 1701-1728
-
-
Tierney, L.1
-
181
-
-
0141817852
-
Multi-locus sequence typing: A tool for global epidemiology
-
Urwin R, Maiden MC (2003) Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11:479-487
-
(2003)
Trends Microbiol
, vol.11
, pp. 479-487
-
-
Urwin, R.1
Maiden, M.C.2
-
182
-
-
0037385669
-
Network analysis of human and simian immunodeficiency virus sequence sets reveals massive recombination resulting in shorter pathways
-
Wain-Hobson S, Renoux-Elbe C, Vartanian JP, Meyerhans A (2003) Network analysis of human and simian immunodeficiency virus sequence sets reveals massive recombination resulting in shorter pathways. J Gen Virol 84:885-895
-
(2003)
J Gen Virol
, vol.84
, pp. 885-895
-
-
Wain-Hobson, S.1
Renoux-Elbe, C.2
Vartanian, J.P.3
Meyerhans, A.4
-
183
-
-
0033955443
-
A comparison of estimators of the population recombination rate
-
Wall JD (2000) A comparison of estimators of the population recombination rate. Mol Biol Evol 17:156-163
-
(2000)
Mol Biol Evol
, vol.17
, pp. 156-163
-
-
Wall, J.D.1
-
184
-
-
0016491430
-
On the number of segregating sites in genetical models without recombination
-
Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256-276
-
(1975)
Theor Popul Biol
, vol.7
, pp. 256-276
-
-
Watterson, G.A.1
-
185
-
-
0043123111
-
RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
-
Wernersson R, Pedersen AG (2003) RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res 31:3537-3539
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3537-3539
-
-
Wernersson, R.1
Pedersen, A.G.2
-
186
-
-
0001857390
-
Optimization alignment: The end of multiple alignment in phylogenetics?
-
Wheeler WC (1996) Optimization alignment: the end of multiple alignment in phylogenetics? Cladistics 12:1-9
-
(1996)
Cladistics
, vol.12
, pp. 1-9
-
-
Wheeler, W.C.1
-
188
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families 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
-
189
-
-
0036667699
-
The genealogy of a sequence subject to purifying selection at multiple sites
-
Williamson S, Orive ME (2002) The genealogy of a sequence subject to purifying selection at multiple sites. Mol Biol Evol 19:1376-1384
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1376-1384
-
-
Williamson, S.1
Orive, M.E.2
-
190
-
-
33645229840
-
Estimating diversifying selection and functional constraint in the presence of recombination
-
Wilson DJ, McVean G (2006) Estimating diversifying selection and functional constraint in the presence of recombination. Genetics 172:1411-1425
-
(2006)
Genetics
, vol.172
, pp. 1411-1425
-
-
Wilson, D.J.1
McVean, G.2
-
191
-
-
8544225780
-
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
-
Wong WS, Yang Z, Goldman N, Nielsen R (2004) Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051
-
(2004)
Genetics
, vol.168
, pp. 1041-1051
-
-
Wong, W.S.1
Yang, Z.2
Goldman, N.3
Nielsen, R.4
-
192
-
-
0036671454
-
The matrix coalescent and an application to human single-nucleotide polymorphisms
-
Wooding S, Rogers A (2002) The matrix coalescent and an application to human single-nucleotide polymorphisms. Genetics 161:1641-1650
-
(2002)
Genetics
, vol.161
, pp. 1641-1650
-
-
Wooding, S.1
Rogers, A.2
-
193
-
-
0037461034
-
TreeSAAP: Selection on amino acid properties using phylogenetic trees
-
Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA (2003) TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics 19:671-672
-
(2003)
Bioinformatics
, vol.19
, pp. 671-672
-
-
Woolley, S.1
Johnson, J.2
Smith, M.J.3
Crandall, K.A.4
McClellan, D.A.5
-
194
-
-
0031766244
-
What amino acid properties affect protein evolution?
-
Xia X, Li WH (1998) What amino acid properties affect protein evolution? J Mol Evol 47:557-564
-
(1998)
J Mol Evol
, vol.47
, pp. 557-564
-
-
Xia, X.1
Li, W.H.2
-
195
-
-
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 13:555-556
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
196
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496-503
-
(2000)
Trends Ecol Evol
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
197
-
-
0033979433
-
Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
-
Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32-43
-
(2000)
Mol Biol Evol
, vol.17
, pp. 32-43
-
-
Yang, Z.1
Nielsen, R.2
-
198
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang Z, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908-917
-
(2002)
Mol Biol Evol
, vol.19
, pp. 908-917
-
-
Yang, Z.1
Nielsen, R.2
-
199
-
-
22844452772
-
Branch-length prior influences Bayesian posterior probabilities of phylogeny
-
Yang Z, Rannala B (2005) Branch-length prior influences Bayesian posterior probabilities of phylogeny. Syst Biol 54:455-470
-
(2005)
Syst Biol
, vol.54
, pp. 455-470
-
-
Yang, Z.1
Rannala, B.2
-
200
-
-
0036134765
-
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
-
Yang Z, Swanson WJ (2002) Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol Biol Evol 19:49-57
-
(2002)
Mol Biol Evol
, vol.19
, pp. 49-57
-
-
Yang, Z.1
Swanson, W.J.2
-
201
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.M.4
-
202
-
-
16344378246
-
Bayes empirical Bayes inference of amino acid sites under positive selection
-
Yang Z, Wong WS, Nielsen R (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107-1118.
-
(2005)
Mol Biol Evol
, vol.22
, pp. 1107-1118
-
-
Yang, Z.1
Wong, W.S.2
Nielsen, R.3
-
203
-
-
0031025677
-
Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods
-
Zhang J, Nei M (1997) Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J Mol Evol 44:S139-S146
-
(1997)
J Mol Evol
, vol.44
-
-
Zhang, J.1
Nei, M.2
-
204
-
-
12444337674
-
Model parameterization, prior distributions, and the general timereversible model in Bayesian phylogenetics
-
Zwickl DJ, Holder MT (2004) Model parameterization, prior distributions, and the general timereversible 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
|