-
1
-
-
15944396106
-
Missing the forest for the trees: phylogenetic compression and its implications for inferring complex evolutionary histories
-
Ané C., Sanderson M. Missing the forest for the trees: phylogenetic compression and its implications for inferring complex evolutionary histories. Syst. Biol. 2005, 54:146-157.
-
(2005)
Syst. Biol.
, vol.54
, pp. 146-157
-
-
Ané, C.1
Sanderson, M.2
-
2
-
-
79960041437
-
Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction
-
Ané C. Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction. Genome Biol. Evol. 2011, 3:246-258.
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 246-258
-
-
Ané, C.1
-
3
-
-
84880947338
-
Networks, expanding evolutionary thinking
-
Bapteste E., van Iersel L., Janke A., Kelchner S., Kelk S., McInerney J.O., Morrison D.A., Nakhleh L., Steel M., Stougie L., Whitfield J. Networks, expanding evolutionary thinking. Trends Genet. 2013, 29:439-441.
-
(2013)
Trends Genet.
, vol.29
, pp. 439-441
-
-
Bapteste, E.1
van Iersel, L.2
Janke, A.3
Kelchner, S.4
Kelk, S.5
McInerney, J.O.6
Morrison, D.A.7
Nakhleh, L.8
Steel, M.9
Stougie, L.10
Whitfield, J.11
-
4
-
-
84939184648
-
Weighted statistical binning: enabling statistically consistent genome-scale phylogenetic analyses
-
Bayzid M.S., Mirarab S., Boussau B., Warnow T. Weighted statistical binning: enabling statistically consistent genome-scale phylogenetic analyses. Plos One 2015, 10:e0129183.
-
(2015)
Plos One
, vol.10
, pp. e0129183
-
-
Bayzid, M.S.1
Mirarab, S.2
Boussau, B.3
Warnow, T.4
-
5
-
-
34948847222
-
A new approach to estimate parameters of speciation models with application to apes
-
Becquet C., Przeworski M. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 2007, 17:1505-1519.
-
(2007)
Genome Res.
, vol.17
, pp. 1505-1519
-
-
Becquet, C.1
Przeworski, M.2
-
6
-
-
84964694545
-
Genome-wide search identifies 1.9 megabases from the polar bear Y chromosome for evolutionary analyses
-
Bidon T., Schreck N., Hailer F., Nilsson M., Janke A. Genome-wide search identifies 1.9 megabases from the polar bear Y chromosome for evolutionary analyses. Genome Biol. 2015, 7:2010-2022.
-
(2015)
Genome Biol.
, vol.7
, pp. 2010-2022
-
-
Bidon, T.1
Schreck, N.2
Hailer, F.3
Nilsson, M.4
Janke, A.5
-
7
-
-
84864697376
-
Inferring species trees directly from Biallelic genetic markers, bypassing gene trees in a full coalescent analysis
-
Bryant D., Bouckaert R., Felsenstein J., Rosenberg N.A., RoyChoudhury A. Inferring species trees directly from Biallelic genetic markers, bypassing gene trees in a full coalescent analysis. Mol. Biol. Evol. 2012, 29:1917-1932.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 1917-1932
-
-
Bryant, D.1
Bouckaert, R.2
Felsenstein, J.3
Rosenberg, N.A.4
RoyChoudhury, A.5
-
8
-
-
67049119180
-
Evidence for an ancient adaptive episode of convergent molecular evolution
-
Castoe T.A., de Koning A.P.J., Kim H.-M., Gu W., Noonan B.P., Naylor G., Jiang Z.J., Parkinson C.L., Pollock D.D. Evidence for an ancient adaptive episode of convergent molecular evolution. Proc. Natl. Acad. Sci. USA 2009, 106:8986-8991.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 8986-8991
-
-
Castoe, T.A.1
de Koning, A.P.J.2
Kim, H.-M.3
Gu, W.4
Noonan, B.P.5
Naylor, G.6
Jiang, Z.J.7
Parkinson, C.L.8
Pollock, D.D.9
-
9
-
-
77953729511
-
Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats
-
Carstens B.C., Dewey T.A. Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Syst. Biol. 2010, 59:400-414.
-
(2010)
Syst. Biol.
, vol.59
, pp. 400-414
-
-
Carstens, B.C.1
Dewey, T.A.2
-
10
-
-
79955117575
-
Bayesian estimation of species trees: a practical guide to optimal sampling and analysis
-
Wiley-Blackwell, New Jersey, L.L. Knowles, L.S. Kubatko (Eds.)
-
Castillo-Ramírez S., et al. Bayesian estimation of species trees: a practical guide to optimal sampling and analysis. Estimating Species Trees: Practical and Theoretical Aspects 2010, 15-33. Wiley-Blackwell, New Jersey. L.L. Knowles, L.S. Kubatko (Eds.).
-
(2010)
Estimating Species Trees: Practical and Theoretical Aspects
, pp. 15-33
-
-
Castillo-Ramírez, S.1
-
11
-
-
84864249563
-
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
-
Chiari Y., Cahais V., Galtier N., Delsuc F. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol. 2012, 10:65.
-
(2012)
BMC Biol.
, vol.10
, pp. 65
-
-
Chiari, Y.1
Cahais, V.2
Galtier, N.3
Delsuc, F.4
-
12
-
-
84917697072
-
Quartet inference from SNP data under the coalescent model
-
Chifman J., Kubatko L. Quartet inference from SNP data under the coalescent model. Bioinformatics 2014, 30:3317-3324.
-
(2014)
Bioinformatics
, vol.30
, pp. 3317-3324
-
-
Chifman, J.1
Kubatko, L.2
-
13
-
-
84944736951
-
A comparative study of SVDquartets and other coalescent-based species tree estimation methods
-
Chou J., Gupta A., Yaduvanshi S., Davidson R., Nute M., Mirarab S., Warnow T. A comparative study of SVDquartets and other coalescent-based species tree estimation methods. BMC Genom. 2015, 16(Suppl. 10):S2.
-
(2015)
BMC Genom.
, vol.16
, pp. S2
-
-
Chou, J.1
Gupta, A.2
Yaduvanshi, S.3
Davidson, R.4
Nute, M.5
Mirarab, S.6
Warnow, T.7
-
14
-
-
80051782566
-
A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases
-
Cummins C.A., McInerney J.O. A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Syst. Biol. 2011, 60:833-844.
-
(2011)
Syst. Biol.
, vol.60
, pp. 833-844
-
-
Cummins, C.A.1
McInerney, J.O.2
-
15
-
-
84944717648
-
Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer
-
Davidson R., Vachaspati P., Mirarab S., Warnow T. Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer. BMC Genom. 2015, 16(Suppl. 10):S1.
-
(2015)
BMC Genom.
, vol.16
, pp. S1
-
-
Davidson, R.1
Vachaspati, P.2
Mirarab, S.3
Warnow, T.4
-
16
-
-
33646928341
-
Discordance of species trees with their most likely gene trees
-
Degnan J.H., Rosenberg N.A. Discordance of species trees with their most likely gene trees. PLoS Genet. 2006, 2:762-768.
-
(2006)
PLoS Genet.
, vol.2
, pp. 762-768
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
17
-
-
84864346710
-
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
-
dos Reis M., Inoue J., Hasegawa M., Asher R.J., Donoghue P.C., Yang Z. Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc. Biol. Sci. 2012, 279:3491-3500.
-
(2012)
Proc. Biol. Sci.
, vol.279
, pp. 3491-3500
-
-
dos Reis, M.1
Inoue, J.2
Hasegawa, M.3
Asher, R.J.4
Donoghue, P.C.5
Yang, Z.6
-
18
-
-
84887717585
-
Agalma, an automated phylogenomics workflow
-
Dunn C.W., Howison M., Zapata F. Agalma, an automated phylogenomics workflow. BMC Bioinform. 2013, 14:330.
-
(2013)
BMC Bioinform.
, vol.14
, pp. 330
-
-
Dunn, C.W.1
Howison, M.2
Zapata, F.3
-
19
-
-
79961039058
-
Testing for ancient admixture between closely related populations
-
Durand E.Y., Patterson N., Reich D., Slatkin M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 2011, 28:2239-2252.
-
(2011)
Mol. Biol. Evol.
, vol.28
, pp. 2239-2252
-
-
Durand, E.Y.1
Patterson, N.2
Reich, D.3
Slatkin, M.4
-
20
-
-
56549103832
-
Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow
-
Eckert A.J., Carstens B.C. Does gene flow destroy phylogenetic signal? The performance of three methods for estimating species phylogenies in the presence of gene flow. Mol. Phylogenet. Evol. 2008, 49:832-842. 10.1016/j.ympev.2008.09.008.
-
(2008)
Mol. Phylogenet. Evol.
, vol.49
, pp. 832-842
-
-
Eckert, A.J.1
Carstens, B.C.2
-
21
-
-
58249100073
-
Is a new and general theory of molecular systematics emerging?
-
Edwards S.V. Is a new and general theory of molecular systematics emerging?. Evolution 2009, 63:1-19.
-
(2009)
Evolution
, vol.63
, pp. 1-19
-
-
Edwards, S.V.1
-
22
-
-
67049159696
-
Natural selection and phylogenetic analysis
-
Edwards S.V. Natural selection and phylogenetic analysis. Proc. Natl. Acad. Sci. USA 2009, 106:8799-8800.
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 8799-8800
-
-
Edwards, S.V.1
-
23
-
-
84946424739
-
Inferring species trees
-
Richard Kliman (Ed.), Encyclopedia of Evolutionary Biology. Elsevier, Amsterdam (in press).
-
Edwards, S.V., 2015. Inferring species trees. In: Richard Kliman (Ed.), Encyclopedia of Evolutionary Biology. Elsevier, Amsterdam (in press).
-
(2015)
-
-
Edwards, S.V.1
-
24
-
-
0024181337
-
Phylogenies and quantitative characters
-
Felsenstein J. Phylogenies and quantitative characters. Annu. Rev. Ecol. Syst. 1988, 19:445-471.
-
(1988)
Annu. Rev. Ecol. Syst.
, vol.19
, pp. 445-471
-
-
Felsenstein, J.1
-
25
-
-
0032805771
-
Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa
-
Gatesy J., O'Grady P., Baker R. Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 1999, 15:271-313.
-
(1999)
Cladistics
, vol.15
, pp. 271-313
-
-
Gatesy, J.1
O'Grady, P.2
Baker, R.3
-
26
-
-
22844438847
-
Hidden likelihood support in genomic data: can forty-five wrongs make a right?
-
Gatesy J., Baker R.H. Hidden likelihood support in genomic data: can forty-five wrongs make a right?. Syst. Biol. 2005, 54:483-492.
-
(2005)
Syst. Biol.
, vol.54
, pp. 483-492
-
-
Gatesy, J.1
Baker, R.H.2
-
27
-
-
84875547630
-
Concatenation versus coalescence versus "concatalescence"
-
Gatesy J., Springer M.S. Concatenation versus coalescence versus "concatalescence". Proc. Natl. Acad. Sci. USA 2013, 110:E1179.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. E1179
-
-
Gatesy, J.1
Springer, M.S.2
-
28
-
-
84908162664
-
Phylogenetic analysis at deep timescales, unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
-
Gatesy J., Springer M.S. Phylogenetic analysis at deep timescales, unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum. Mol. Phylogenet. Evol. 2014, 80:231-266.
-
(2014)
Mol. Phylogenet. Evol.
, vol.80
, pp. 231-266
-
-
Gatesy, J.1
Springer, M.S.2
-
29
-
-
0344430855
-
Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses
-
Goldman N. Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Syst. Biol. 1990, 39:345-361.
-
(1990)
Syst. Biol.
, vol.39
, pp. 345-361
-
-
Goldman, N.1
-
31
-
-
77950806408
-
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
-
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
-
(2010)
Syst. Biol.
, vol.59
, pp. 307-321
-
-
Guindon, S.1
Dufayard, J.F.2
Lefort, V.3
Anisimova, M.4
Hordijk, W.5
Gascuel, O.6
-
32
-
-
47349109604
-
Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations
-
Hallström B.M., Janke A. Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations. BMC Evol. Biol. 2008, 8:162.
-
(2008)
BMC Evol. Biol.
, vol.8
, pp. 162
-
-
Hallström, B.M.1
Janke, A.2
-
33
-
-
78649382339
-
Mammalian evolution may not be strictly bifurcating
-
Hallström B.M., Janke A. Mammalian evolution may not be strictly bifurcating. Mol. Biol. Evol. 2010, 27:2804-2816.
-
(2010)
Mol. Biol. Evol.
, vol.27
, pp. 2804-2816
-
-
Hallström, B.M.1
Janke, A.2
-
34
-
-
77249086587
-
Bayesian inference of species trees from multilocus data
-
Heled J., Drummond A.J. Bayesian inference of species trees from multilocus data. Mol. Biology Evol. 2010, 27:570-580.
-
(2010)
Mol. Biology Evol.
, vol.27
, pp. 570-580
-
-
Heled, J.1
Drummond, A.J.2
-
35
-
-
33847253862
-
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model
-
Hobolth A., Christensen O.F., Mailund T., Schierup M.H. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet. 2007, 3:e7.
-
(2007)
PLoS Genet.
, vol.3
, pp. e7
-
-
Hobolth, A.1
Christensen, O.F.2
Mailund, T.3
Schierup, M.H.4
-
36
-
-
0028270434
-
The marsupial mitochondrial genome and the evolution of placental mammals
-
Janke A., Feldmaier-Fuchs G., Thomas W.K., Von Haeseler A., Pääbo S. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 1994, 137:243-256.
-
(1994)
Genetics
, vol.137
, pp. 243-256
-
-
Janke, A.1
Feldmaier-Fuchs, G.2
Thomas, W.K.3
Von Haeseler, A.4
Pääbo, S.5
-
37
-
-
84917708482
-
Whole-genome analyses resolve early branches in the tree of life of modern birds
-
Jarvis E.D., Mirarab S., Aberer A.J., Li B., Houde P., Li C., Ho S.Y.W., Faircloth B.C., Nabholz B., Howard J.T., Suh A., Weber C.C., da Fonseca R.R., Li J.W., Zhang F., Li H., Zhou L., Narula N., Liu L., Ganapathy G., Boussau B., Bayzid M.S., Zavidovych V., Subramanian S., Gabaldon T., Capella-Gutierrez S., Huerta-Cepas J., Rekepalli B., Munch K., Schierup M., Lindow B., Warren W.C., Ray D., Green R.E., Bruford M.W., Zhan X.J., Dixon A., Li S.B., Li N., Huang Y.H., Derryberry E.P., Bertelsen M.F., Sheldon F.H., Brumfield R.T., Mello C.V., Lovell P.V., Wirthlin M., Schneider M.P.C., Prosdocimi F., Samaniego J.A., Velazquez A.M.V., Alfaro-Nunez A., Campos P.F., Petersen B., Sicheritz-Ponten T., Pas A., Bailey T., Scofield P., Bunce M., Lambert D.M., Zhou Q., Perelman P., Driskell A.C., Shapiro B., Xiong Z.J., Zeng Y.L., Liu S.P., Li Z.Y., Liu B.H., Wu K., Xiao J., Yinqi X., Zheng Q.M., Zhang Y., Yang H.M., Wang J., Smeds L., Rheindt F.E., Braun M., Fjeldsa J., Orlando L., Barker F.K., Jonsson K.A., Johnson W., Koepfli K.P., O'Brien S., Haussler D., Ryder O.A., Rahbek C., Willerslev E., Graves G.R., Glenn T.C., McCormack J., Burt D., Ellegren H., Alstrom P., Edwards S.V., Stamatakis A., Mindell D.P., Cracraft J., Braun E.L., Warnow T., Jun W., Gilbert M.T.P., Zhang G.J. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 2014, 346:1320-1331.
-
(2014)
Science
, vol.346
, pp. 1320-1331
-
-
Jarvis, E.D.1
Mirarab, S.2
Aberer, A.J.3
Li, B.4
Houde, P.5
Li, C.6
Ho, S.Y.W.7
Faircloth, B.C.8
Nabholz, B.9
Howard, J.T.10
Suh, A.11
Weber, C.C.12
da Fonseca, R.R.13
Li, J.W.14
Zhang, F.15
Li, H.16
Zhou, L.17
Narula, N.18
Liu, L.19
Ganapathy, G.20
Boussau, B.21
Bayzid, M.S.22
Zavidovych, V.23
Subramanian, S.24
Gabaldon, T.25
Capella-Gutierrez, S.26
Huerta-Cepas, J.27
Rekepalli, B.28
Munch, K.29
Schierup, M.30
Lindow, B.31
Warren, W.C.32
Ray, D.33
Green, R.E.34
Bruford, M.W.35
Zhan, X.J.36
Dixon, A.37
Li, S.B.38
Li, N.39
Huang, Y.H.40
Derryberry, E.P.41
Bertelsen, M.F.42
Sheldon, F.H.43
Brumfield, R.T.44
Mello, C.V.45
Lovell, P.V.46
Wirthlin, M.47
Schneider, M.P.C.48
Prosdocimi, F.49
Samaniego, J.A.50
Velazquez, A.M.V.51
Alfaro-Nunez, A.52
Campos, P.F.53
Petersen, B.54
Sicheritz-Ponten, T.55
Pas, A.56
Bailey, T.57
Scofield, P.58
Bunce, M.59
Lambert, D.M.60
Zhou, Q.61
Perelman, P.62
Driskell, A.C.63
Shapiro, B.64
Xiong, Z.J.65
Zeng, Y.L.66
Liu, S.P.67
Li, Z.Y.68
Liu, B.H.69
Wu, K.70
Xiao, J.71
Yinqi, X.72
Zheng, Q.M.73
Zhang, Y.74
Yang, H.M.75
Wang, J.76
Smeds, L.77
Rheindt, F.E.78
Braun, M.79
Fjeldsa, J.80
Orlando, L.81
Barker, F.K.82
Jonsson, K.A.83
Johnson, W.84
Koepfli, K.P.85
O'Brien, S.86
Haussler, D.87
Ryder, O.A.88
Rahbek, C.89
Willerslev, E.90
Graves, G.R.91
Glenn, T.C.92
McCormack, J.93
Burt, D.94
Ellegren, H.95
Alstrom, P.96
Edwards, S.V.97
Stamatakis, A.98
Mindell, D.P.99
more..
-
38
-
-
84924299935
-
Speciation with gene flow in equids despite extensive chromosomal plasticity
-
Jónsson H., Schubert M., Seguin-Orlando A., Ginolhac A., Petersen L., Fumagalli M., Albrechtsen A., Petersen B., Korneliussen T.S., Vilstrup J.T., Lear T., Myka J.L., Lundquist J., Miller D.C., Alfarhan A.H., Alquraishi S.A., Al-Rasheid K.A.S., Stagegaard J., Strauss G., Bertelsen M.F., Sicheritz-Ponten T., Antczak D.F., Bailey E., Nielsen R., Willerslev E., Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proc. Natl. Acad. Sci. USA 2014, 111:18655-18660.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 18655-18660
-
-
Jónsson, H.1
Schubert, M.2
Seguin-Orlando, A.3
Ginolhac, A.4
Petersen, L.5
Fumagalli, M.6
Albrechtsen, A.7
Petersen, B.8
Korneliussen, T.S.9
Vilstrup, J.T.10
Lear, T.11
Myka, J.L.12
Lundquist, J.13
Miller, D.C.14
Alfarhan, A.H.15
Alquraishi, S.A.16
Al-Rasheid, K.A.S.17
Stagegaard, J.18
Strauss, G.19
Bertelsen, M.F.20
Sicheritz-Ponten, T.21
Antczak, D.F.22
Bailey, E.23
Nielsen, R.24
Willerslev, E.25
Orlando, L.26
more..
-
40
-
-
0002556819
-
On the genealogy of large populations
-
Kingman J.F.C. On the genealogy of large populations. J. Appl. Probab. 1982, 27-43.
-
(1982)
J. Appl. Probab.
, pp. 27-43
-
-
Kingman, J.F.C.1
-
41
-
-
0034530345
-
Origins of the coalescent: 1974-1982
-
Kingman J.F.C. Origins of the coalescent: 1974-1982. Genetics 2000, 156:1461-1463.
-
(2000)
Genetics
, vol.156
, pp. 1461-1463
-
-
Kingman, J.F.C.1
-
42
-
-
84866147332
-
Full modeling versus summarizing gene-tree uncertainty, method choice and species-tree accuracy
-
Knowles L.L., Lanier H.C., Klimov P.B., He Q. Full modeling versus summarizing gene-tree uncertainty, method choice and species-tree accuracy. Mol. Phylogenet. Evol. 2012, 65:501-509.
-
(2012)
Mol. Phylogenet. Evol.
, vol.65
, pp. 501-509
-
-
Knowles, L.L.1
Lanier, H.C.2
Klimov, P.B.3
He, Q.4
-
43
-
-
33847302458
-
Inconsistency of phylogenetic estimates from concatenated data under coalescence
-
Kubatko L.S., Degnan J.H. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 2007, 56:17-24.
-
(2007)
Syst. Biol.
, vol.56
, pp. 17-24
-
-
Kubatko, L.S.1
Degnan, J.H.2
-
44
-
-
63549118031
-
STEM, species tree estimation using maximum likelihood for gene trees under coalescence
-
Kubatko L.S., Carstens B.C., Knowles L.L. STEM, species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 2009, 25:971-973.
-
(2009)
Bioinformatics
, vol.25
, pp. 971-973
-
-
Kubatko, L.S.1
Carstens, B.C.2
Knowles, L.L.3
-
45
-
-
84875653134
-
Coalescent-based genome analyses resolve the early branches of the euarchontoglires
-
Kumar V., Hallström B.M., Janke A. Coalescent-based genome analyses resolve the early branches of the euarchontoglires. PLoS One 2013, 8:e60019.
-
(2013)
PLoS One
, vol.8
, pp. e60019
-
-
Kumar, V.1
Hallström, B.M.2
Janke, A.3
-
46
-
-
84904966117
-
Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow
-
Kutschera V.E., Bidon T., Hailer F., Rodi J.L., Fain S.R., Janke A. Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow. Mol. Biol. Evol. 2014, 31:2004-2017.
-
(2014)
Mol. Biol. Evol.
, vol.31
, pp. 2004-2017
-
-
Kutschera, V.E.1
Bidon, T.2
Hailer, F.3
Rodi, J.L.4
Fain, S.R.5
Janke, A.6
-
47
-
-
84860552871
-
Is recombination a problem for species-tree analyses?
-
Lanier H.C., Knowles L.L. Is recombination a problem for species-tree analyses?. Syst. Biol. 2012, 61:691-701.
-
(2012)
Syst. Biol.
, vol.61
, pp. 691-701
-
-
Lanier, H.C.1
Knowles, L.L.2
-
48
-
-
84888140829
-
How low can you go? The effects of mutation rate on the accuracy of species-tree estimation
-
Lanier H.C., Huang H., Knowles L.L. How low can you go? The effects of mutation rate on the accuracy of species-tree estimation. Mol. Phylogenet. Evol. 2014, 70:112-119.
-
(2014)
Mol. Phylogenet. Evol.
, vol.70
, pp. 112-119
-
-
Lanier, H.C.1
Huang, H.2
Knowles, L.L.3
-
49
-
-
79951561454
-
The accuracy of species tree estimation under simulation, a comparison of methods
-
Leaché A.D., Rannala B. The accuracy of species tree estimation under simulation, a comparison of methods. Syst. Biol. 2011, 60:126-137.
-
(2011)
Syst. Biol.
, vol.60
, pp. 126-137
-
-
Leaché, A.D.1
Rannala, B.2
-
50
-
-
84887319003
-
The influence of gene flow on species tree estimation: A simulation study
-
Leaché A.D., Harris R.B., Rannala B., Yang Z. The influence of gene flow on species tree estimation: A simulation study. Syst. Biol. 2014, 63(1):17-30. 10.1093/sysbio/syt049.
-
(2014)
Syst. Biol.
, vol.63
, Issue.1
, pp. 17-30
-
-
Leaché, A.D.1
Harris, R.B.2
Rannala, B.3
Yang, Z.4
-
51
-
-
84888626247
-
High-throughput genomic data in systematics and phylogenetics
-
Lemmon E.M., Lemmon A.R. High-throughput genomic data in systematics and phylogenetics. Annu. Rev. Ecol. Evol. Syst. 2013, 44:99-121.
-
(2013)
Annu. Rev. Ecol. Evol. Syst.
, vol.44
, pp. 99-121
-
-
Lemmon, E.M.1
Lemmon, A.R.2
-
52
-
-
0002948868
-
Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data
-
Lewis, P.O., 1998. Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data. Mol. Syst. Plants II. Springer, pp. 132-163.
-
(1998)
Mol. Syst. Plants II. Springer
, pp. 132-163
-
-
Lewis, P.O.1
-
53
-
-
84881508358
-
One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods
-
Liang D., Shen X.X., Zhang P. One thousand two hundred ninety nuclear genes from a genome-wide survey support lungfishes as the sister group of tetrapods. Mol. Biol. Evol. 2013, 30:1803-1807.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 1803-1807
-
-
Liang, D.1
Shen, X.X.2
Zhang, P.3
-
54
-
-
70349417912
-
Phylogenetic analysis in the anomaly zone
-
Liu L., Edwards S.V. Phylogenetic analysis in the anomaly zone. Syst. Biol. 2009, 58:452-460.
-
(2009)
Syst. Biol.
, vol.58
, pp. 452-460
-
-
Liu, L.1
Edwards, S.V.2
-
55
-
-
84943549799
-
Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree"
-
Liu L., Edwards S.V. Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree". Science 2015, 350:171. 10.1126/science.aaa7343.
-
(2015)
Science
, vol.350
, pp. 171
-
-
Liu, L.1
Edwards, S.V.2
-
56
-
-
77951961553
-
Phybase, an R package for species tree analysis
-
Liu L., Yu L. Phybase, an R package for species tree analysis. Bioinformatics 2010, 26:962-963.
-
(2010)
Bioinformatics
, vol.26
, pp. 962-963
-
-
Liu, L.1
Yu, L.2
-
57
-
-
70349425459
-
Estimating species phylogenies using coalescence times among sequences
-
Liu L., Yu L., Pearl D.K., Edwards S.V. Estimating species phylogenies using coalescence times among sequences. Syst. Biol. 2009, 58:468-477.
-
(2009)
Syst. Biol.
, vol.58
, pp. 468-477
-
-
Liu, L.1
Yu, L.2
Pearl, D.K.3
Edwards, S.V.4
-
58
-
-
77957686501
-
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
-
Liu L., Yu L., Edwards S.V. A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol. Biol. 2010, 10:302.
-
(2010)
BMC Evol. Biol.
, vol.10
, pp. 302
-
-
Liu, L.1
Yu, L.2
Edwards, S.V.3
-
59
-
-
84903386054
-
An HMM-based comparative genomic framework for detecting introgression in eukaryotes
-
Liu K.J., Dai J., Truong K., Song Y., Kohn M.H., Nakhleh L. An HMM-based comparative genomic framework for detecting introgression in eukaryotes. Plos Comput. Biol. 2014, 10:e1003649.
-
(2014)
Plos Comput. Biol.
, vol.10
, pp. e1003649
-
-
Liu, K.J.1
Dai, J.2
Truong, K.3
Song, Y.4
Kohn, M.H.5
Nakhleh, L.6
-
60
-
-
84965093929
-
Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting
-
Liu L., Xi Z., Davis C.C. Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting. Mol. Biol. Evol. 2015, 32:791-805.
-
(2015)
Mol. Biol. Evol.
, vol.32
, pp. 791-805
-
-
Liu, L.1
Xi, Z.2
Davis, C.C.3
-
61
-
-
84949317694
-
Estimating phylogenetic trees from genome-scale data
-
Article first published online: 14 Apr 2015
-
Liu L., Xi Z., Wu S., Davis C.C., Edwards S.V. Estimating phylogenetic trees from genome-scale data. Ann. NY Acad. Sci. 2015, Article first published online: 14 Apr 2015. 10.1111/nyas.12747.
-
(2015)
Ann. NY Acad. Sci.
-
-
Liu, L.1
Xi, Z.2
Wu, S.3
Davis, C.C.4
Edwards, S.V.5
-
62
-
-
34547396004
-
The frailty of adaptive hypotheses for the origins of organismal complexity
-
Lynch M. The frailty of adaptive hypotheses for the origins of organismal complexity. Proc. Natl. Acad. Sci. USA 2007, 104(1):8597-8604.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, Issue.1
, pp. 8597-8604
-
-
Lynch, M.1
-
63
-
-
13144283628
-
A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints
-
Martin D.P., Posada D., Crandall K.A., Williamson C. A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. Aids Res. Human Retrovir. 2005, 21:98-102.
-
(2005)
Aids Res. Human Retrovir.
, vol.21
, pp. 98-102
-
-
Martin, D.P.1
Posada, D.2
Crandall, K.A.3
Williamson, C.4
-
64
-
-
70450265498
-
Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design
-
McCormack J.E., Huang H.T., Knowles L.L. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 2009, 58:501-508.
-
(2009)
Syst. Biol.
, vol.58
, pp. 501-508
-
-
McCormack, J.E.1
Huang, H.T.2
Knowles, L.L.3
-
65
-
-
84859530730
-
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis
-
McCormack J.E., Faircloth B.C., Crawford N.G., Gowaty P.A., Brumfield R.T., Glenn T.C. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species tree analysis. Genome Res. 2012, 22:746-754.
-
(2012)
Genome Res.
, vol.22
, pp. 746-754
-
-
McCormack, J.E.1
Faircloth, B.C.2
Crawford, N.G.3
Gowaty, P.A.4
Brumfield, R.T.5
Glenn, T.C.6
-
66
-
-
84872008491
-
A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species
-
Mailund T., Halager A.E., Westergaard M., Dutheil J.Y., Munch K., Andersen L.N., Lunter G., Prufer K., Scally A., Hobolth A., Schierup M.H. A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet. 2012, 8:e1003125.
-
(2012)
PLoS Genet.
, vol.8
, pp. e1003125
-
-
Mailund, T.1
Halager, A.E.2
Westergaard, M.3
Dutheil, J.Y.4
Munch, K.5
Andersen, L.N.6
Lunter, G.7
Prufer, K.8
Scally, A.9
Hobolth, A.10
Schierup, M.H.11
-
67
-
-
84917708481
-
Statistical binning enables an accurate coalescent-based estimation of the avian tree
-
Mirarab S., Bayzid M.S., Boussau B., Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science 2014, 346:1240463.
-
(2014)
Science
, vol.346
, pp. 1240463
-
-
Mirarab, S.1
Bayzid, M.S.2
Boussau, B.3
Warnow, T.4
-
68
-
-
84907019380
-
ASTRAL, genome-scale coalescent-based species tree estimation
-
Mirarab S., Reaz R., Bayzid M.S., Zimmermann T., Swenson M.S., Warnow T. ASTRAL, genome-scale coalescent-based species tree estimation. Bioinformatics 2014, 30:i541-i548.
-
(2014)
Bioinformatics
, vol.30
, pp. i541-i548
-
-
Mirarab, S.1
Reaz, R.2
Bayzid, M.S.3
Zimmermann, T.4
Swenson, M.S.5
Warnow, T.6
-
69
-
-
84931034856
-
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
-
Mirarab S., Warnow T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics 2015, 31:i44-i52.
-
(2015)
Bioinformatics
, vol.31
, pp. i44-i52
-
-
Mirarab, S.1
Warnow, T.2
-
70
-
-
84909606775
-
Phylogenomics resolves the timing and pattern of insect evolution
-
Misof B., Liu S., Meusemann K., Peters R.S., Donath A., Mayer C., Frandsen P.B., Ware J., Flouri T., Beutel R.G., Niehuis O., Petersen M., Izquierdo-Carrasco F., Wappler T., Rust J., Aberer A.J., Aspock U., Aspock H., Bartel D., Blanke A., Berger S., Bohm A., Buckley T.R., Calcott B., Chen J., Friedrich F., Fukui M., Fujita M., Greve C., Grobe P., Gu S., Huang Y., Jermiin L.S., Kawahara A.Y., Krogmann L., Kubiak M., Lanfear R., Letsch H., Li Y., Li Z., Li J., Lu H., Machida R., Mashimo Y., Kapli P., McKenna D.D., Meng G., Nakagaki Y., Navarrete-Heredia J.L., Ott M., Ou Y., Pass G., Podsiadlowski L., Pohl H., von Reumont B.M., Schutte K., Sekiya K., Shimizu S., Slipinski A., Stamatakis A., Song W., Su X., Szucsich N.U., Tan M., Tan X., Tang M., Tang J., Timelthaler G., Tomizuka S., Trautwein M., Tong X., Uchifune T., Walzl M.G., Wiegmann B.M., Wilbrandt J., Wipfler B., Wong T.K., Wu Q., Wu G., Xie Y., Yang S., Yang Q., Yeates D.K., Yoshizawa K., Zhang Q., Zhang R., Zhang W., Zhang Y., Zhao J., Zhou C., Zhou L., Ziesmann T., Zou S., Li Y., Xu X., Zhang Y., Yang H., Wang J., Wang J., Kjer K.M., Zhou X. Phylogenomics resolves the timing and pattern of insect evolution. Science 2014, 346:763-767.
-
(2014)
Science
, vol.346
, pp. 763-767
-
-
Misof, B.1
Liu, S.2
Meusemann, K.3
Peters, R.S.4
Donath, A.5
Mayer, C.6
Frandsen, P.B.7
Ware, J.8
Flouri, T.9
Beutel, R.G.10
Niehuis, O.11
Petersen, M.12
Izquierdo-Carrasco, F.13
Wappler, T.14
Rust, J.15
Aberer, A.J.16
Aspock, U.17
Aspock, H.18
Bartel, D.19
Blanke, A.20
Berger, S.21
Bohm, A.22
Buckley, T.R.23
Calcott, B.24
Chen, J.25
Friedrich, F.26
Fukui, M.27
Fujita, M.28
Greve, C.29
Grobe, P.30
Gu, S.31
Huang, Y.32
Jermiin, L.S.33
Kawahara, A.Y.34
Krogmann, L.35
Kubiak, M.36
Lanfear, R.37
Letsch, H.38
Li, Y.39
Li, Z.40
Li, J.41
Lu, H.42
Machida, R.43
Mashimo, Y.44
Kapli, P.45
McKenna, D.D.46
Meng, G.47
Nakagaki, Y.48
Navarrete-Heredia, J.L.49
Ott, M.50
Ou, Y.51
Pass, G.52
Podsiadlowski, L.53
Pohl, H.54
von Reumont, B.M.55
Schutte, K.56
Sekiya, K.57
Shimizu, S.58
Slipinski, A.59
Stamatakis, A.60
Song, W.61
Su, X.62
Szucsich, N.U.63
Tan, M.64
Tan, X.65
Tang, M.66
Tang, J.67
Timelthaler, G.68
Tomizuka, S.69
Trautwein, M.70
Tong, X.71
Uchifune, T.72
Walzl, M.G.73
Wiegmann, B.M.74
Wilbrandt, J.75
Wipfler, B.76
Wong, T.K.77
Wu, Q.78
Wu, G.79
Xie, Y.80
Yang, S.81
Yang, Q.82
Yeates, D.K.83
Yoshizawa, K.84
Zhang, Q.85
Zhang, R.86
Zhang, W.87
Zhang, Y.88
Zhao, J.89
Zhou, C.90
Zhou, L.91
Ziesmann, T.92
Zou, S.93
Li, Y.94
Xu, X.95
Zhang, Y.96
Yang, H.97
Wang, J.98
Wang, J.99
more..
-
71
-
-
0035861441
-
Resolution of the early placental mammal radiation using Bayesian phylogenetics
-
Murphy W.J., Eizirik E., O'Brien S.J., Madsen O., Scally M., Douady C.J., Teeling E., Ryder O.A., Stanhope M.J., de Jong W.W., Springer M.S. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 2001, 294:2348-2351.
-
(2001)
Science
, vol.294
, pp. 2348-2351
-
-
Murphy, W.J.1
Eizirik, E.2
O'Brien, S.J.3
Madsen, O.4
Scally, M.5
Douady, C.J.6
Teeling, E.7
Ryder, O.A.8
Stanhope, M.J.9
de Jong, W.W.10
Springer, M.S.11
-
72
-
-
79959662697
-
Jaatha: A fast composite-likelihood approach to estimate demographic parameters
-
Naduvilezhath L., Rose L.E., Metzler D. Jaatha: A fast composite-likelihood approach to estimate demographic parameters. Mol. Ecol. 2011, 20:2709-2723. 10.1111/j.1365-294X.2011.05131.x.
-
(2011)
Mol. Ecol.
, vol.20
, pp. 2709-2723
-
-
Naduvilezhath, L.1
Rose, L.E.2
Metzler, D.3
-
73
-
-
84888137812
-
Computational approaches to species phylogeny inference and gene tree reconciliation
-
Nakhleh L. Computational approaches to species phylogeny inference and gene tree reconciliation. Trends Ecol. Evol. 2013, 28:719-728.
-
(2013)
Trends Ecol. Evol.
, vol.28
, pp. 719-728
-
-
Nakhleh, L.1
-
74
-
-
0034623005
-
T-Coffee: a novel method for fast and accurate multiple sequence alignment
-
Notredame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302:205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
75
-
-
0023822631
-
Relationships between gene trees and species trees
-
Pamilo P., Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5:568-583.
-
(1988)
Mol. Biol. Evol.
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Nei, M.2
-
76
-
-
84878084517
-
Inference of reticulate evolutionary histories by maximum likelihood, the performance of information criteria
-
Park H.J., Nakhleh L. Inference of reticulate evolutionary histories by maximum likelihood, the performance of information criteria. BMC Bioinform. 2012, 13(Suppl. 19):S12.
-
(2012)
BMC Bioinform.
, vol.13
, pp. S12
-
-
Park, H.J.1
Nakhleh, L.2
-
78
-
-
79953716259
-
Resolving difficult phylogenetic questions: why more sequences are not enough
-
Philippe H., Brinkmann H., Lavrov D.V., Littlewood D.T.J., Manuel M., Wörheide G., et al. Resolving difficult phylogenetic questions: why more sequences are not enough. PLoS Biol. 2011, 9(3):e1000602.
-
(2011)
PLoS Biol.
, vol.9
, Issue.3
, pp. e1000602
-
-
Philippe, H.1
Brinkmann, H.2
Lavrov, D.V.3
Littlewood, D.T.J.4
Manuel, M.5
Wörheide, G.6
-
79
-
-
0035923699
-
Evaluation of methods for detecting recombination from DNA sequences: computer simulations
-
Posada D., Crandall K.A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. USA 2001, 98:13757-13762.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 13757-13762
-
-
Posada, D.1
Crandall, K.A.2
-
80
-
-
0036183042
-
The effect of recombination on the accuracy of phylogeny estimation
-
Posada D., Crandall K.A. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 2002, 54:396-402.
-
(2002)
J. Mol. Evol.
, vol.54
, pp. 396-402
-
-
Posada, D.1
Crandall, K.A.2
-
82
-
-
0030928378
-
Seq-Gen, an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A., Grassly N.C. Seq-Gen, an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1997, 13:235-238.
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
83
-
-
0041817551
-
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
-
Rannala B., Yang Z. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 2003, 164:1645-1656.
-
(2003)
Genetics
, vol.164
, pp. 1645-1656
-
-
Rannala, B.1
Yang, Z.2
-
84
-
-
39749111875
-
OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics
-
Ranwez V., Delsuc F., Ranwez S., Belkhir K., Tilak M.-K., Douzery E.J. OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol. Biol. 2007, 7:241. 10.1186/1471-2148-7-241.
-
(2007)
BMC Evol. Biol.
, vol.7
, pp. 241
-
-
Ranwez, V.1
Delsuc, F.2
Ranwez, S.3
Belkhir, K.4
Tilak, M.-K.5
Douzery, E.J.6
-
85
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson D.F., Foulds L.R. Comparison of phylogenetic trees. Math. Biosci. 1981, 53:131-147.
-
(1981)
Math. Biosci.
, vol.53
, pp. 131-147
-
-
Robinson, D.F.1
Foulds, L.R.2
-
86
-
-
84890335523
-
Discordance of species trees with their most likely gene trees: a unifying principle
-
Rosenberg N.A. Discordance of species trees with their most likely gene trees: a unifying principle. Mol. Biol. Evol. 2013, 30:2709-2713.
-
(2013)
Mol. Biol. Evol.
, vol.30
, pp. 2709-2713
-
-
Rosenberg, N.A.1
-
87
-
-
0036245438
-
Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
-
Rosenberg N.A., Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 2002, 3:380-390.
-
(2002)
Nat. Rev. Genet.
, vol.3
, pp. 380-390
-
-
Rosenberg, N.A.1
Nordborg, M.2
-
88
-
-
47749087905
-
Discordance of species trees with their most likely gene trees, the case of five taxa
-
Rosenberg N.A., Tao R. Discordance of species trees with their most likely gene trees, the case of five taxa. Syst. Biol. 2008, 57:131-140.
-
(2008)
Syst. Biol.
, vol.57
, pp. 131-140
-
-
Rosenberg, N.A.1
Tao, R.2
-
89
-
-
45449097556
-
Recombination and phylogeny: effects and detection
-
Ruths D., Nakhleh L. Recombination and phylogeny: effects and detection. Int. J. Bioinform. Res. Appl. 2005, 1:202-212.
-
(2005)
Int. J. Bioinform. Res. Appl.
, vol.1
, pp. 202-212
-
-
Ruths, D.1
Nakhleh, L.2
-
90
-
-
84863230553
-
Insights into hominid evolution from the gorilla genome sequence
-
Scally A., Dutheil J.Y., Hillier L.W., Jordan G.E., Goodhead I., Herrero J., Hobolth A., Lappalainen T., Mailund T., Marques-Bonet T., McCarthy S., Montgomery S.H., Schwalie P.C., Tang Y.A., Ward M.C., Xue Y.L., Yngvadottir B., Alkan C., Andersen L.N., Ayub Q., Ball E.V., Beal K., Bradley B.J., Chen Y., Clee C.M., Fitzgerald S., Graves T.A., Gu Y., Heath P., Heger A., Karakoc E., Kolb-Kokocinski A., Laird G.K., Lunter G., Meader S., Mort M., Mullikin J.C., Munch K., O'Connor T.D., Phillips A.D., Prado-Martinez J., Rogers A.S., Sajjadian S., Schmidt D., Shaw K., Simpson J.T., Stenson P.D., Turner D.J., Vigilant L., Vilella A.J., Whitener W., Zhu B.L., Cooper D.N., de Jong P., Dermitzakis E.T., Eichler E.E., Flicek P., Goldman N., Mundy N.I., Ning Z.M., Odom D.T., Ponting C.P., Quail M.A., Ryder O.A., Searle S.M., Warren W.C., Wilson R.K., Schierup M.H., Rogers J., Tyler-Smith C., Durbin R. Insights into hominid evolution from the gorilla genome sequence. Nature 2012, 483:169-175.
-
(2012)
Nature
, vol.483
, pp. 169-175
-
-
Scally, A.1
Dutheil, J.Y.2
Hillier, L.W.3
Jordan, G.E.4
Goodhead, I.5
Herrero, J.6
Hobolth, A.7
Lappalainen, T.8
Mailund, T.9
Marques-Bonet, T.10
McCarthy, S.11
Montgomery, S.H.12
Schwalie, P.C.13
Tang, Y.A.14
Ward, M.C.15
Xue, Y.L.16
Yngvadottir, B.17
Alkan, C.18
Andersen, L.N.19
Ayub, Q.20
Ball, E.V.21
Beal, K.22
Bradley, B.J.23
Chen, Y.24
Clee, C.M.25
Fitzgerald, S.26
Graves, T.A.27
Gu, Y.28
Heath, P.29
Heger, A.30
Karakoc, E.31
Kolb-Kokocinski, A.32
Laird, G.K.33
Lunter, G.34
Meader, S.35
Mort, M.36
Mullikin, J.C.37
Munch, K.38
O'Connor, T.D.39
Phillips, A.D.40
Prado-Martinez, J.41
Rogers, A.S.42
Sajjadian, S.43
Schmidt, D.44
Shaw, K.45
Simpson, J.T.46
Stenson, P.D.47
Turner, D.J.48
Vigilant, L.49
Vilella, A.J.50
Whitener, W.51
Zhu, B.L.52
Cooper, D.N.53
de Jong, P.54
Dermitzakis, E.T.55
Eichler, E.E.56
Flicek, P.57
Goldman, N.58
Mundy, N.I.59
Ning, Z.M.60
Odom, D.T.61
Ponting, C.P.62
Quail, M.A.63
Ryder, O.A.64
Searle, S.M.65
Warren, W.C.66
Wilson, R.K.67
Schierup, M.H.68
Rogers, J.69
Tyler-Smith, C.70
Durbin, R.71
more..
-
91
-
-
84930960341
-
Coalescence vs. concatenation, sophisticated analyses vs. first principles applied to rooting the angiosperms
-
Simmons M.P., Gatesy J. Coalescence vs. concatenation, sophisticated analyses vs. first principles applied to rooting the angiosperms. Mol. Phylogenet. Evol. 2015, 91:98-122.
-
(2015)
Mol. Phylogenet. Evol.
, vol.91
, pp. 98-122
-
-
Simmons, M.P.1
Gatesy, J.2
-
92
-
-
33645234370
-
The concordance of gene trees and species trees at two linked loci
-
Slatkin M., Pollack J.L. The concordance of gene trees and species trees at two linked loci. Genetics 2006, 172:1979-1984.
-
(2006)
Genetics
, vol.172
, pp. 1979-1984
-
-
Slatkin, M.1
Pollack, J.L.2
-
93
-
-
40049112246
-
Phyutility, a phyloinformatics tool for trees, alignments and molecular data
-
Smith S.A., Dunn C.W. Phyutility, a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics 2008, 24:715-716.
-
(2008)
Bioinformatics
, vol.24
, pp. 715-716
-
-
Smith, S.A.1
Dunn, C.W.2
-
94
-
-
84884681647
-
Analyzing and synthesizing phylogenies using tree alignment graphs
-
Smith S.A., Brown J.W., Hinchliff C.E. Analyzing and synthesizing phylogenies using tree alignment graphs. Plos Comput. Biol. 2013, 9:e1003223.
-
(2013)
Plos Comput. Biol.
, vol.9
, pp. e1003223
-
-
Smith, S.A.1
Brown, J.W.2
Hinchliff, C.E.3
-
95
-
-
84866289853
-
Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
-
Song S., Liu L., Edwards S.V., Wu S. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc. Natl. Acad. Sci. USA 2012, 109:14942-14947.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 14942-14947
-
-
Song, S.1
Liu, L.2
Edwards, S.V.3
Wu, S.4
-
96
-
-
84899919331
-
Land plant origins and coalescence confusion
-
Springer M.S., Gatesy J. Land plant origins and coalescence confusion. Trends Plant Sci. 2014, 19:267-269.
-
(2014)
Trends Plant Sci.
, vol.19
, pp. 267-269
-
-
Springer, M.S.1
Gatesy, J.2
-
98
-
-
84899553363
-
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
-
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014, 30:1312-1313.
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
99
-
-
84946399166
-
Exploring tree-like and non-tree-like patterns using genome sequences: an example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh
-
Stenz N.W.M., Larget B., Baum D.A., Ané C. Exploring tree-like and non-tree-like patterns using genome sequences: an example using the inbreeding plant species Arabidopsis thaliana (L.) Heynh. Syst. Biol. 2015, 64:809-823.
-
(2015)
Syst. Biol.
, vol.64
, pp. 809-823
-
-
Stenz, N.W.M.1
Larget, B.2
Baum, D.A.3
Ané, C.4
-
100
-
-
84940641284
-
The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds
-
Suh A., Smeds L., Ellegren H. The dynamics of incomplete lineage sorting across the ancient adaptive radiation of neoavian birds. PLoS Biol. 2015, 13:e1002224.
-
(2015)
PLoS Biol.
, vol.13
, pp. e1002224
-
-
Suh, A.1
Smeds, L.2
Ellegren, H.3
-
101
-
-
0035527406
-
Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
-
Swofford D.L., Waddell P.J., Huelsenbeck J.P., Foster P.G., Lewis P.O., Rogers J.S. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 2001, 50:525-539.
-
(2001)
Syst. Biol.
, vol.50
, pp. 525-539
-
-
Swofford, D.L.1
Waddell, P.J.2
Huelsenbeck, J.P.3
Foster, P.G.4
Lewis, P.O.5
Rogers, J.S.6
-
102
-
-
0021066244
-
Evolutionary relationship of DNA sequences in finite populations
-
Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics 1983, 105:437-460.
-
(1983)
Genetics
, vol.105
, pp. 437-460
-
-
Tajima, F.1
-
103
-
-
0022390691
-
Gene genealogy and variance of interpopulational nucleotide differences
-
Takahata N., Nei M. Gene genealogy and variance of interpopulational nucleotide differences. Genetics 1985, 110:325-344.
-
(1985)
Genetics
, vol.110
, pp. 325-344
-
-
Takahata, N.1
Nei, M.2
-
104
-
-
51349098340
-
PhyloNet, a software package for analyzing and reconstructing reticulate evolutionary relationships
-
Than C., Ruths D., Nakhleh L. PhyloNet, a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinform. 2008, 9:322.
-
(2008)
BMC Bioinform.
, vol.9
, pp. 322
-
-
Than, C.1
Ruths, D.2
Nakhleh, L.3
-
105
-
-
55049088739
-
Developing markers for multilocus phylogenetics in non-model organisms, a test case with turtles
-
Thomson R.C., Shedlock A.M., Edwards S.V., Shaffer H.B. Developing markers for multilocus phylogenetics in non-model organisms, a test case with turtles. Mol. Phylogenet. Evol. 2008, 49:514-525.
-
(2008)
Mol. Phylogenet. Evol.
, vol.49
, pp. 514-525
-
-
Thomson, R.C.1
Shedlock, A.M.2
Edwards, S.V.3
Shaffer, H.B.4
-
106
-
-
84889090318
-
Phylogenomic analyses elucidate the evolutionary relationships of bats
-
Tsagkogeorga G., Parker J., Stupka E., Cotton J.A., Rossiter S.J. Phylogenomic analyses elucidate the evolutionary relationships of bats. Curr. Biol. 2013, 23:2262-2267.
-
(2013)
Curr. Biol.
, vol.23
, pp. 2262-2267
-
-
Tsagkogeorga, G.1
Parker, J.2
Stupka, E.3
Cotton, J.A.4
Rossiter, S.J.5
-
107
-
-
84855873417
-
Testing hypotheses about the sister group of the Passeriformes using an independent 30 locus dataset
-
Wang N., Braun E.L., Kimball R.T. Testing hypotheses about the sister group of the Passeriformes using an independent 30 locus dataset. Mol. Biol. Evol. 2012, 29:737-750.
-
(2012)
Mol. Biol. Evol.
, vol.29
, pp. 737-750
-
-
Wang, N.1
Braun, E.L.2
Kimball, R.T.3
-
108
-
-
84906264612
-
KDETREES: non-parametric estimation of phylogenetic tree distributions
-
Weyenberg G., Huggins P.M., Schardl C.L., Howe D.K., Yoshida R. KDETREES: non-parametric estimation of phylogenetic tree distributions. Bioinformatics 2014, 30:2280-2287.
-
(2014)
Bioinformatics
, vol.30
, pp. 2280-2287
-
-
Weyenberg, G.1
Huggins, P.M.2
Schardl, C.L.3
Howe, D.K.4
Yoshida, R.5
-
109
-
-
73649129187
-
Fine-scale phylogenetic discordance across the house mouse genome
-
White M.A., Ane C., Dewey C.N., Larget B.R., Payseur B.A. Fine-scale phylogenetic discordance across the house mouse genome. PLoS Genet. 2009, 5:e1000729.
-
(2009)
PLoS Genet.
, vol.5
, pp. e1000729
-
-
White, M.A.1
Ane, C.2
Dewey, C.N.3
Larget, B.R.4
Payseur, B.A.5
-
111
-
-
84909619344
-
Phylotranscriptomic analysis of the origin and early diversification of land plants
-
Wickett N.J., Mirarab S., Nguyen N., Warnow T., Carpenter E., Matasci N., Ayyampalayam S., Barker M.S., Burleigh J.G., Gitzendanner M.A., Ruhfel B.R., Wafula E., Der J.P., Graham S.W., Mathews S., Melkonian M., Soltis D.E., Soltis P.S., Miles N.W., Rothfels C.J., Pokorny L., Shaw A.J., DeGironimo L., Stevenson D.W., Surek B., Villarreal J.C., Roure B., Philippe H., dePamphilis C.W., Chen T., Deyholos M.K., Baucom R.S., Kutchan T.M., Augustin M.M., Wang J., Zhang Y., Tian Z., Yan Z., Wu X., Sun X., Wong G.K., Leebens-Mack J. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc. Natl. Acad. Sci. USA 2014, 111:E4859-E4868.
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. E4859-E4868
-
-
Wickett, N.J.1
Mirarab, S.2
Nguyen, N.3
Warnow, T.4
Carpenter, E.5
Matasci, N.6
Ayyampalayam, S.7
Barker, M.S.8
Burleigh, J.G.9
Gitzendanner, M.A.10
Ruhfel, B.R.11
Wafula, E.12
Der, J.P.13
Graham, S.W.14
Mathews, S.15
Melkonian, M.16
Soltis, D.E.17
Soltis, P.S.18
Miles, N.W.19
Rothfels, C.J.20
Pokorny, L.21
Shaw, A.J.22
DeGironimo, L.23
Stevenson, D.W.24
Surek, B.25
Villarreal, J.C.26
Roure, B.27
Philippe, H.28
dePamphilis, C.W.29
Chen, T.30
Deyholos, M.K.31
Baucom, R.S.32
Kutchan, T.M.33
Augustin, M.M.34
Wang, J.35
Zhang, Y.36
Tian, Z.37
Yan, Z.38
Wu, X.39
Sun, X.40
Wong, G.K.41
Leebens-Mack, J.42
more..
-
112
-
-
84875513968
-
Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity
-
Wu S., Song S., Liu L., Edwards S.V. Reply to Gatesy and Springer: the multispecies coalescent model can effectively handle recombination and gene tree heterogeneity. Proc. Natl. Acad. Sci. USA 2013, 110:E1180.
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. E1180
-
-
Wu, S.1
Song, S.2
Liu, L.3
Edwards, S.V.4
-
113
-
-
84894052682
-
Phylogenomics and coalescent analyses resolve extant seed plant relationships
-
Xi Z., Rest J.S., Davis C.C. Phylogenomics and coalescent analyses resolve extant seed plant relationships. PLoS One 2013, 8:e80870.
-
(2013)
PLoS One
, vol.8
, pp. e80870
-
-
Xi, Z.1
Rest, J.S.2
Davis, C.C.3
-
114
-
-
84919947905
-
Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies
-
Xi Z., Liu L., Rest J.S., Davis C.C. Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies. Syst. Biol. 2014, 63:919-932.
-
(2014)
Syst. Biol.
, vol.63
, pp. 919-932
-
-
Xi, Z.1
Liu, L.2
Rest, J.S.3
Davis, C.C.4
-
115
-
-
84934296789
-
Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
-
Xi Z., Liu L., Davis C.C. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased. Mol. Phylogenet. Evol. 2015, 92:63-71.
-
(2015)
Mol. Phylogenet. Evol.
, vol.92
, pp. 63-71
-
-
Xi, Z.1
Liu, L.2
Davis, C.C.3
-
116
-
-
84944739954
-
A maximum pseudo-likelihood approach for phylogenetic networks
-
Yu Y., Nakhleh L. A maximum pseudo-likelihood approach for phylogenetic networks. BMC Genom. 2015, 16(Suppl. 10):S10.
-
(2015)
BMC Genom.
, vol.16
, pp. S10
-
-
Yu, Y.1
Nakhleh, L.2
-
117
-
-
84883284590
-
Origin of land plants using the multispecies coalescent model
-
Zhong B., Liu L., Yan Z., Penny D. Origin of land plants using the multispecies coalescent model. Trends Plant Sci. 2013, 18:492-495.
-
(2013)
Trends Plant Sci.
, vol.18
, pp. 492-495
-
-
Zhong, B.1
Liu, L.2
Yan, Z.3
Penny, D.4
-
118
-
-
84899921887
-
The multispecies coalescent model and land plant origins, a reply to Springer and Gatesy
-
Zhong B., Liu L., Penny D. The multispecies coalescent model and land plant origins, a reply to Springer and Gatesy. Trends Plant Sci. 2014, 19:270-272.
-
(2014)
Trends Plant Sci.
, vol.19
, pp. 270-272
-
-
Zhong, B.1
Liu, L.2
Penny, D.3
-
119
-
-
84906251283
-
Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
-
Zwickl D.J., Stein J.C., Wing R.A., Ware D., Sanderson M.J. Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Syst. Biol. 2014, 63:645-659.
-
(2014)
Syst. Biol.
, vol.63
, pp. 645-659
-
-
Zwickl, D.J.1
Stein, J.C.2
Wing, R.A.3
Ware, D.4
Sanderson, M.J.5
|