-
1
-
-
84863707192
-
Simulation of molecular data under diverse evolutionary scenarios
-
10.1371/journal.pcbi.1002495, 3364941, 22693434
-
Arenas M. Simulation of molecular data under diverse evolutionary scenarios. PLoS Comput Biol 2012, 8(5):e1002495. 10.1371/journal.pcbi.1002495, 3364941, 22693434.
-
(2012)
PLoS Comput Biol
, vol.8
, Issue.5
-
-
Arenas, M.1
-
2
-
-
84855963371
-
Computer simulations: tools for population and evolutionary genetics
-
Hoban S, Bertorelle G, Gaggiotti OE. Computer simulations: tools for population and evolutionary genetics. Nat Rev Genet 2011, 13(2):110-122.
-
(2011)
Nat Rev Genet
, vol.13
, Issue.2
, pp. 110-122
-
-
Hoban, S.1
Bertorelle, G.2
Gaggiotti, O.E.3
-
4
-
-
48849105171
-
Computational reconstruction of ancestral DNA sequences
-
10.1007/978-1-59745-581-7_11, 18629667
-
Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Computational reconstruction of ancestral DNA sequences. Methods Mol Biol 2008, 422:171-184. 10.1007/978-1-59745-581-7_11, 18629667.
-
(2008)
Methods Mol Biol
, vol.422
, pp. 171-184
-
-
Blanchette, M.1
Diallo, A.B.2
Green, E.D.3
Miller, W.4
Haussler, D.5
-
5
-
-
60149104693
-
PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy
-
10.1093/bioinformatics/btn651, 19098028
-
Brown JM, ElDabaje R. PuMA: Bayesian analysis of partitioned (and unpartitioned) model adequacy. Bioinformatics 2009, 25(4):537-538. 10.1093/bioinformatics/btn651, 19098028.
-
(2009)
Bioinformatics
, vol.25
, Issue.4
, pp. 537-538
-
-
Brown, J.M.1
ElDabaje, R.2
-
6
-
-
0027526039
-
Statistical tests of models of DNA substitution
-
10.1007/BF00166252, 7679448
-
Goldman N. Statistical tests of models of DNA substitution. J Mol Evol 1993, 36(2):182-198. 10.1007/BF00166252, 7679448.
-
(1993)
J Mol Evol
, vol.36
, Issue.2
, pp. 182-198
-
-
Goldman, N.1
-
7
-
-
0030928378
-
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A, Grass NC. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci 1997, 13(3):235-238.
-
(1997)
Comput Appl Biosci
, vol.13
, Issue.3
, pp. 235-238
-
-
Rambaut, A.1
Grass, N.C.2
-
8
-
-
34547803197
-
PAML 4: Phylogenetic Analysis by Maximum Likelihood
-
10.1093/molbev/msm088, 17483113
-
Yang Z. PAML 4: Phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol 2007, 24(8):1586-1591. 10.1093/molbev/msm088, 17483113.
-
(2007)
Mol Biol Evol
, vol.24
, Issue.8
, pp. 1586-1591
-
-
Yang, Z.1
-
9
-
-
15844406550
-
HyPhy: hypothesis testing using phylogenies
-
10.1093/bioinformatics/bti079, 15509596
-
Kosakovsky Pond SL, Frost SDW, Muse SV. HyPhy: hypothesis testing using phylogenies. Bioinformatics 2005, 21(5):676-679. 10.1093/bioinformatics/bti079, 15509596.
-
(2005)
Bioinformatics
, vol.21
, Issue.5
, pp. 676-679
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.W.2
Muse, S.V.3
-
11
-
-
0036909632
-
Estimating divergence times from molecular data on phylogenetic and population genetic timescales
-
Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu Rev Ecol Evol Systemat 2002, 33:707-740.
-
(2002)
Annu Rev Ecol Evol Systemat
, vol.33
, pp. 707-740
-
-
Arbogast, B.S.1
Edwards, S.V.2
Wakeley, J.3
Beerli, P.4
Slowinski, J.B.5
-
12
-
-
84864530626
-
Bayesian phylogenetics with BEAUti and the BEAST 1.7
-
10.1093/molbev/mss075, 3408070, 22367748
-
Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012, 29(8):1969-1973. 10.1093/molbev/mss075, 3408070, 22367748.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.8
, pp. 1969-1973
-
-
Drummond, A.J.1
Suchard, M.A.2
Xie, D.3
Rambaut, A.4
-
13
-
-
33344465800
-
Relaxed phylogenetics and dating with confidence
-
10.1371/journal.pbio.0040088, 1395354, 16683862
-
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol 2006, 4(5):e88. 10.1371/journal.pbio.0040088, 1395354, 16683862.
-
(2006)
PLoS Biol
, vol.4
, Issue.5
-
-
Drummond, A.J.1
Ho, S.Y.W.2
Phillips, M.J.3
Rambaut, A.4
-
14
-
-
77956488734
-
Bayesian random local clocks, or one rate to rule them all
-
10.1186/1741-7007-8-114, 2949620, 20807414
-
Drummond A, Suchard M. Bayesian random local clocks, or one rate to rule them all. BMC Biol 2010, 8:114. 10.1186/1741-7007-8-114, 2949620, 20807414.
-
(2010)
BMC Biol
, vol.8
, pp. 114
-
-
Drummond, A.1
Suchard, M.2
-
15
-
-
70349675664
-
Bayesian Phylogeography Finds Its Roots
-
10.1371/journal.pcbi.1000520, 2740835, 19779555
-
Lemey P, Rambaut A, Drummond AJ, Suchard MA. Bayesian Phylogeography Finds Its Roots. PLoS Comput Biol 2009, 5(9):e1000520. 10.1371/journal.pcbi.1000520, 2740835, 19779555.
-
(2009)
PLoS Comput Biol
, vol.5
, Issue.9
-
-
Lemey, P.1
Rambaut, A.2
Drummond, A.J.3
Suchard, M.A.4
-
16
-
-
84555188616
-
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics
-
10.1093/sysbio/syr100, 3243739, 21963610
-
Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA. BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol 2012, 61:170-173. 10.1093/sysbio/syr100, 3243739, 21963610.
-
(2012)
Syst Biol
, vol.61
, pp. 170-173
-
-
Ayres, D.L.1
Darling, A.2
Zwickl, D.J.3
Beerli, P.4
Holder, M.T.5
Lewis, P.O.6
Huelsenbeck, J.P.7
Ronquist, F.8
Swofford, D.L.9
Cummings, M.P.10
Rambaut, A.11
Suchard, M.A.12
-
17
-
-
0001143041
-
Nineteen dubious ways to compute the exponential of a matrix
-
Moler C, Loan CV. Nineteen dubious ways to compute the exponential of a matrix. SIAM Rev 1978, 20:801-836.
-
(1978)
SIAM Rev
, vol.20
, pp. 801-836
-
-
Moler, C.1
Loan, C.V.2
-
18
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
10.1007/BF02101694, 3934395, Yano Ta
-
Hasegawa M, Kishino H, . Yano Ta Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 1985, 22:160-174. 10.1007/BF02101694, 3934395, Yano Ta.
-
(1985)
J Mol Evol
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
-
19
-
-
0027157960
-
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
-
Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993, 10(3):512-526.
-
(1993)
Mol Biol Evol
, vol.10
, Issue.3
, pp. 512-526
-
-
Tamura, K.1
Nei, M.2
-
20
-
-
0002671410
-
Some probabilistic and statistical problems in the analysis of DNA sequences
-
Tavaré S
-
Tavaré S Some probabilistic and statistical problems in the analysis of DNA sequences. Lect Math Life Sci (American Mathematical Society) 1986, 17:57-86. Tavaré S.
-
(1986)
Lect Math Life Sci (American Mathematical Society)
, vol.17
, pp. 57-86
-
-
-
21
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman N, Yang Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 1994, 11(5):725-736.
-
(1994)
Mol Biol Evol
, vol.11
, Issue.5
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
22
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse SV, Gaut BS. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 1994, 11(5):715-724.
-
(1994)
Mol Biol Evol
, vol.11
, Issue.5
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
23
-
-
0000228203
-
A model of evolutionary change in proteins
-
Washington, D.C., USA: Citeseer, National Biomedical Research Foundation
-
Dayhoff MO, Schwartz RM. A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure 1978, Washington, D.C., USA: Citeseer, National Biomedical Research Foundation.
-
(1978)
Atlas of Protein Sequence and Structure
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
-
24
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8(3):275-282.
-
(1992)
Comput Appl Biosci
, vol.8
, Issue.3
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
25
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
10.1073/pnas.89.22.10915, 50453, 1438297
-
Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci 1992, 89(22):10915-10919. 10.1073/pnas.89.22.10915, 50453, 1438297.
-
(1992)
Proc Natl Acad Sci
, vol.89
, Issue.22
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
26
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
10.1093/oxfordjournals.molbev.a003851, 11319253
-
Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18(5):691-699. 10.1093/oxfordjournals.molbev.a003851, 11319253.
-
(2001)
Mol Biol Evol
, vol.18
, Issue.5
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
27
-
-
45849154166
-
An improved general amino acid replacement matrix
-
10.1093/molbev/msn067, 18367465
-
Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol 2008, 25(7):1307-1320. 10.1093/molbev/msn067, 18367465.
-
(2008)
Mol Biol Evol
, vol.25
, Issue.7
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
28
-
-
0030451420
-
Among-site rate variation and its impact on phylogenetic analyses
-
10.1016/0169-5347(96)10041-0, 21237881
-
Yang Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol 1996, 11(9):367-372. 10.1016/0169-5347(96)10041-0, 21237881.
-
(1996)
Trends Ecol Evol
, vol.11
, Issue.9
, pp. 367-372
-
-
Yang, Z.1
-
29
-
-
0029068893
-
Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites
-
Gu X, Fu YX, Li WH. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 1995, 12(4):546-557.
-
(1995)
Mol Biol Evol
, vol.12
, Issue.4
, pp. 546-557
-
-
Gu, X.1
Fu, Y.X.2
Li, W.H.3
-
30
-
-
80051469138
-
Ancient hybridization and an Irish origin for the modern polar bear matriline
-
10.1016/j.cub.2011.05.058, 21737280
-
Edwards CJ, Suchard MA, Lemey P, Welch JJ, Barnes I, Fulton TL, Barnett R, O'Connell TC, Coxon P, Monaghan N, Valdiosera CE, Lorenzen ED, Willerslev E, Baryshnikov GF, Rambaut A, Thomas MG, Bradley DG, Shapiro B. Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol 2011, 21:1251-1258. 10.1016/j.cub.2011.05.058, 21737280.
-
(2011)
Curr Biol
, vol.21
, pp. 1251-1258
-
-
Edwards, C.J.1
Suchard, M.A.2
Lemey, P.3
Welch, J.J.4
Barnes, I.5
Fulton, T.L.6
Barnett, R.7
O'Connell, T.C.8
Coxon, P.9
Monaghan, N.10
Valdiosera, C.E.11
Lorenzen, E.D.12
Willerslev, E.13
Baryshnikov, G.F.14
Rambaut, A.15
Thomas, M.G.16
Bradley, D.G.17
Shapiro, B.18
-
31
-
-
84900422268
-
Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography
-
Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography. Syst Biol 2014, [http://sysbio.oxfordjournals.org/content/early/2014/04/21/sysbio.syu015].
-
(2014)
Syst Biol
-
-
Bielejec, F.1
Lemey, P.2
Baele, G.3
Rambaut, A.4
Suchard, M.A.5
-
32
-
-
73349096292
-
Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0
-
10.1093/molbev/msp174, 2760465, 19651852
-
Strope CL, Abel K, Scott SD, Moriyama EN. Biological sequence simulation for testing complex evolutionary hypotheses: indel-Seq-Gen version 2.0. Mol Biol Evol 2009, 26(11):2581-2593. 10.1093/molbev/msp174, 2760465, 19651852.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.11
, pp. 2581-2593
-
-
Strope, C.L.1
Abel, K.2
Scott, S.D.3
Moriyama, E.N.4
-
33
-
-
79955109754
-
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment
-
10.1186/1471-2105-12-104, 3102636, 21504561
-
Sipos B, Massingham T, Jordan G, Goldman N. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. BMC Bioinformatics 2011, 12:104. [http://www.biomedcentral.com/1471-2105/12/104], 10.1186/1471-2105-12-104, 3102636, 21504561.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 104
-
-
Sipos, B.1
Massingham, T.2
Jordan, G.3
Goldman, N.4
-
34
-
-
38349167557
-
Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography
-
10.1186/1471-2105-8-458, 2206059, 18028540
-
Arenas M, Posada D. Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics 2007, 8:458. 10.1186/1471-2105-8-458, 2206059, 18028540.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 458
-
-
Arenas, M.1
Posada, D.2
-
35
-
-
77749261568
-
Coalescent simulation of intracodon recombination
-
10.1534/genetics.109.109736, 2828723, 19933876
-
Arenas M, Posada D. Coalescent simulation of intracodon recombination. Genetics 2010, 184(2):429-437. 10.1534/genetics.109.109736, 2828723, 19933876.
-
(2010)
Genetics
, vol.184
, Issue.2
, pp. 429-437
-
-
Arenas, M.1
Posada, D.2
-
36
-
-
67749108209
-
INDELible: a flexible simulator of biological sequence evolution
-
10.1093/molbev/msp098, 2712615, 19423664
-
Fletcher W, Yang Z. INDELible: a flexible simulator of biological sequence evolution. Mol Biol Evol 2009, 26(8):1879-1888. 10.1093/molbev/msp098, 2712615, 19423664.
-
(2009)
Mol Biol Evol
, vol.26
, Issue.8
, pp. 1879-1888
-
-
Fletcher, W.1
Yang, Z.2
-
37
-
-
28944454501
-
DNA assembly with gaps (Dawg): simulating sequence evolution
-
Cartwright RA. DNA assembly with gaps (Dawg): simulating sequence evolution. Bioinformatics 2005, 21(Suppl 3):i31-i38.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 3
-
-
Cartwright, R.A.1
-
38
-
-
3042649996
-
Mesquite: a modular system for evolutionary analysis
-
Maddison WP, Maddison D. Mesquite: a modular system for evolutionary analysis. 2011, [http://mesquiteproject.org].
-
(2011)
-
-
Maddison, W.P.1
Maddison, D.2
-
39
-
-
0031857684
-
Rose: generating sequence families
-
10.1093/bioinformatics/14.2.157, 9545448
-
Stoye J, Evers D, Meyer F. Rose: generating sequence families. Bioinformatics 1998, 14(2):157-163. 10.1093/bioinformatics/14.2.157, 9545448.
-
(1998)
Bioinformatics
, vol.14
, Issue.2
, pp. 157-163
-
-
Stoye, J.1
Evers, D.2
Meyer, F.3
-
40
-
-
84890067204
-
Protein evolution along phylogenetic histories under structurally constrained substitution models
-
10.1093/bioinformatics/btt530, 24037213
-
Arenas M, Dos Santos HG, Posada D, Bastolla U. Protein evolution along phylogenetic histories under structurally constrained substitution models. Bioinformatics 2013, 29(23):3020-3028. 10.1093/bioinformatics/btt530, 24037213.
-
(2013)
Bioinformatics
, vol.29
, Issue.23
, pp. 3020-3028
-
-
Arenas, M.1
Dos Santos, H.G.2
Posada, D.3
Bastolla, U.4
-
41
-
-
84858406580
-
ALF-a simulation framework for genome evolution
-
10.1093/molbev/msr268, 3341827, 22160766
-
Dalquen DA, Anisimova M, Gonnet GH, Dessimoz C. ALF-a simulation framework for genome evolution. Mol Biol Evol 2012, 29(4):1115-1123. 10.1093/molbev/msr268, 3341827, 22160766.
-
(2012)
Mol Biol Evol
, vol.29
, Issue.4
, pp. 1115-1123
-
-
Dalquen, D.A.1
Anisimova, M.2
Gonnet, G.H.3
Dessimoz, C.4
-
42
-
-
43849112140
-
GENOMEPOP: a program to simulate genomes in populations
-
10.1186/1471-2105-9-223, 2386491, 18447924
-
Carvajal-Rodriguez A. GENOMEPOP: a program to simulate genomes in populations. BMC Bioinformatics 2008, 9:223. 10.1186/1471-2105-9-223, 2386491, 18447924.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 223
-
-
Carvajal-Rodriguez, A.1
-
43
-
-
0034491799
-
SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography
-
10.1093/jhered/91.6.506, 11218093
-
Excoffier L, Novembre J, Schneider S. SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J Hered 2000, 91(6):506-509. 10.1093/jhered/91.6.506, 11218093.
-
(2000)
J Hered
, vol.91
, Issue.6
, pp. 506-509
-
-
Excoffier, L.1
Novembre, J.2
Schneider, S.3
-
44
-
-
27644471132
-
SIMPROT: using an empirically determined indel distribution in simulations of protein evolution
-
10.1186/1471-2105-6-236, 1261159, 16188037
-
Pang A, Smith AD, Nuin PA, Tillier ER. SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics 2005, 6:236. 10.1186/1471-2105-6-236, 1261159, 16188037.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 236
-
-
Pang, A.1
Smith, A.D.2
Nuin, P.A.3
Tillier, E.R.4
-
45
-
-
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. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol 2000, 50(4):348-358.
-
(2000)
J Mol Evol
, vol.50
, Issue.4
, pp. 348-358
-
-
Adachi, J.1
Waddell, P.J.2
Martin, W.3
Hasegawa, M.4
-
46
-
-
77950658657
-
FLU, an amino acid substitution model for influenza proteins
-
10.1186/1471-2148-10-99, 2873421, 20384985
-
Dang C, Le Q, Gascuel O, Le V. FLU, an amino acid substitution model for influenza proteins. BMC Evol Biol 2010, 10:99. [http://www.biomedcentral.com/1471-2148/10/99], 10.1186/1471-2148-10-99, 2873421, 20384985.
-
(2010)
BMC Evol Biol
, vol.10
, pp. 99
-
-
Dang, C.1
Le, Q.2
Gascuel, O.3
Le, V.4
-
47
-
-
0029974748
-
Model of amino acid substitution in proteins encoded by mitochondrial DNA
-
10.1007/BF02498640, 8642615
-
Adachi J, Hasegawa M. Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 1996, 42(4):459-468. 10.1007/BF02498640, 8642615.
-
(1996)
J Mol Evol
, vol.42
, Issue.4
, pp. 459-468
-
-
Adachi, J.1
Hasegawa, M.2
-
48
-
-
0003552989
-
-
t. 1, National Biomedical Research Foundation 1965. (US) NBRF
-
Dayhoff M, Eck R, . (US) NBRF Atlas of Protein Sequence and Structure 1965 t. 1, National Biomedical Research Foundation 1965. [http://books.google.be/books?id=9Hp5nAEACAAJ], (US) NBRF.
-
Atlas of Protein Sequence and Structure 1965
-
-
Dayhoff, M.1
Eck, R.2
-
49
-
-
33845904407
-
MtArt: a new model of amino acid replacement for Arthropoda
-
Abascal F, Posada D, Zardoya R. MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol 2007, 24:1-5.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1-5
-
-
Abascal, F.1
Posada, D.2
Zardoya, R.3
-
50
-
-
0031694349
-
Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders
-
10.1007/PL00006389, 9732458
-
Cao Y, Janke A, Waddell PJ, Westerman M, Takenaka O, Murata S, Okada N, Paabo S, Hasegawa M. Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J Mol Evol 1998, 47(3):307-322. 10.1007/PL00006389, 9732458.
-
(1998)
J Mol Evol
, vol.47
, Issue.3
, 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
-
52
-
-
67349159068
-
MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies
-
10.1016/j.ympev.2009.01.011, 19475713
-
Rota-Stabelli O, Yang Z, Telford MJ. MtZoa: a general mitochondrial amino acid substitutions model for animal evolutionary studies. Mol Phylogenet Evol 2009, 52:268-272. 10.1016/j.ympev.2009.01.011, 19475713.
-
(2009)
Mol Phylogenet Evol
, vol.52
, pp. 268-272
-
-
Rota-Stabelli, O.1
Yang, Z.2
Telford, M.J.3
-
53
-
-
0034922289
-
Modeling amino acid replacement
-
10.1089/10665270050514918, 11382360
-
Muller T, Vingron M. Modeling amino acid replacement. J Comput Biol 2000, 7(6):761-776. 10.1089/10665270050514918, 11382360.
-
(2000)
J Comput Biol
, vol.7
, Issue.6
, pp. 761-776
-
-
Muller, T.1
Vingron, M.2
-
54
-
-
0036017382
-
RtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
-
10.1007/s00239-001-2304-y, 12165843
-
Dimmic MW, Rest JS, Mindell DP, Goldstein RA. rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol 2002, 55:65-73. 10.1007/s00239-001-2304-y, 12165843.
-
(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
-
55
-
-
39849090643
-
HIV-specific probabilistic models of protein evolution
-
10.1371/journal.pone.0000503, 1876811, 17551583
-
Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, Kosakovsky Pond SL. HIV-specific probabilistic models of protein evolution. PLoS ONE 2007, 2(6):e503. 10.1371/journal.pone.0000503, 1876811, 17551583.
-
(2007)
PLoS ONE
, vol.2
, Issue.6
-
-
Nickle, D.C.1
Heath, L.2
Jensen, M.A.3
Gilbert, P.B.4
Mullins, J.I.5
Kosakovsky Pond, S.L.6
-
56
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
10.1007/BF01734359, 7288891
-
Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981, 17:368-376. 10.1007/BF01734359, 7288891.
-
(1981)
J Mol Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
57
-
-
80054941662
-
Purifying selection can obscure the ancient age of viral lineages
-
10.1093/molbev/msr170, 3247791, 21705379
-
Wertheim JO, Kosakovsky Pond SL. Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol 2011, 28(12):3355-3365. 10.1093/molbev/msr170, 3247791, 21705379.
-
(2011)
Mol Biol Evol
, vol.28
, Issue.12
, pp. 3355-3365
-
-
Wertheim, J.O.1
Kosakovsky Pond, S.L.2
-
58
-
-
77955011960
-
Phylogeography takes a relaxed random walk in continuous space and time
-
10.1093/molbev/msq067, 2915639, 20203288
-
Lemey P, Rambaut A, Welch JJ, Suchard MA. Phylogeography takes a relaxed random walk in continuous space and time. Mol Biol Evol 2010, 27(8):1877-85. 10.1093/molbev/msq067, 2915639, 20203288.
-
(2010)
Mol Biol Evol
, vol.27
, Issue.8
, pp. 1877-1885
-
-
Lemey, P.1
Rambaut, A.2
Welch, J.J.3
Suchard, M.A.4
|