-
1
-
-
42149157760
-
Broad phylogenomic sampling improves resolution of the animal tree of life
-
1:CAS:528:DC%2BD1cXksFSju7k%3D 18322464 doi:10.1038/nature06614
-
Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, et al.Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 2008; 452(7188):745-9. doi: 10.1038/nature06614.
-
(2008)
Nature
, vol.452
, Issue.7188
, pp. 745-749
-
-
Dunn, C.W.1
Hejnol, A.2
Matus, D.Q.3
Pang, K.4
Browne, W.E.5
Smith, S.A.6
-
2
-
-
80053132393
-
Phylogenomics reveals deep molluscan relationships
-
1:CAS:528:DC%2BC3MXhtFers7fE 4024475 21892190 doi:10.1038/nature10382
-
Kocot KM, Cannon JT, Todt C, Citarella MR, Kohn AB, Meyer A, et al. Phylogenomics reveals deep molluscan relationships. Nature. 2011; 477:452-6. doi: 10.1038/nature10382.
-
(2011)
Nature
, vol.477
, pp. 452-456
-
-
Kocot, K.M.1
Cannon, J.T.2
Todt, C.3
Citarella, M.R.4
Kohn, A.B.5
Meyer, A.6
-
3
-
-
83555166100
-
Resolving the evolutionary relationships of molluscs with phylogenomic tools
-
1:CAS:528:DC%2BC3MXhtlOmsrnJ 22031330 doi:10.1038/nature10526
-
Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SCS, Rouse GW, et al.Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 2011; 480:364-7. doi: 10.1038/nature10526.
-
(2011)
Nature
, vol.480
, pp. 364-367
-
-
Smith, S.A.1
Wilson, N.G.2
Goetz, F.E.3
Feehery, C.4
Andrade, S.C.S.5
Rouse, G.W.6
-
4
-
-
84868678250
-
A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia
-
doi:10.1371/journal.pone.0048990
-
Fong JJ, Brown JM, Fujita MK, Boussau B. A phylogenomic approach to vertebrate phylogeny supports a turtle-archosaur affinity and a possible paraphyletic lissamphibia. PLoS ONE. 2012; 7(11):48990. doi: 10.1371/journal.pone.0048990.
-
(2012)
PLoS ONE
, vol.7
, Issue.11
-
-
Fong, J.J.1
Brown, J.M.2
Fujita, M.K.3
Boussau, B.4
-
5
-
-
84886287737
-
Phylogenomics resolves evolutionary relationships among ants, bees, and wasps
-
1:CAS:528:DC%2BC3sXhsFOltrzN 24094856 doi:10.1016/j.cub.2013.08.050
-
Johnson BR, Borowiec ML, Chiu JC, Lee EK, Atallah J, Ward PS. Phylogenomics resolves evolutionary relationships among ants, bees, and wasps. Curr Biol. 2013; 23:2058-062. doi: 10.1016/j.cub.2013.08.050.
-
(2013)
Curr Biol
, vol.23
, pp. 2058-2062
-
-
Johnson, B.R.1
Borowiec, M.L.2
Chiu, J.C.3
Lee, E.K.4
Atallah, J.5
Ward, P.S.6
-
6
-
-
84890056203
-
The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution
-
3920664 24337300 doi:10.1126/science.1242592
-
Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, et al.The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science. 2013; 342:1242592. doi: 10.1126/science.1242592.
-
(2013)
Science
, vol.342
-
-
Ryan, J.F.1
Pang, K.2
Schnitzler, C.E.3
Nguyen, A.D.4
Moreland, R.T.5
Simmons, D.K.6
-
7
-
-
84883213635
-
Making the impossible possible: Rooting the tree of placental mammals
-
1:CAS:528:DC%2BC3sXhtlals7bO 23813980 doi:10.1093/molbev/mst118
-
Teeling EC, Hedges SB. Making the impossible possible: Rooting the tree of placental mammals. Mol Biol Evol. 2013; 30(9):1999-2000. doi: 10.1093/molbev/mst118. http://mbe.oxfordjournals.org/content/30/9/1999.full.pdf+html.
-
(2013)
Mol Biol Evol
, vol.30
, Issue.9
, pp. 1999-2000
-
-
Teeling, E.C.1
Hedges, S.B.2
-
8
-
-
84917708482
-
Whole-genome analyses resolve early branches in the tree of life of modern birds
-
1:CAS:528:DC%2BC2cXitVCgs7%2FK 4405904 25504713 doi:10.1126/science.1253451
-
Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, et al.Whole-genome analyses resolve early branches in the tree of life of modern birds. Science. 2014; 346(6215):1320-31. doi: 10.1126/science.1253451. http://www.sciencemag.org/content/346/6215/1320.full.pdf.
-
(2014)
Science
, vol.346
, Issue.6215
, pp. 1320-1331
-
-
Jarvis, E.D.1
Mirarab, S.2
Aberer, A.J.3
Li, B.4
Houde, P.5
Li, C.6
-
9
-
-
84909619344
-
Phylotranscriptomic analysis of the origin and early diversification of land plants
-
doi:10.1073/pnas.1323926111
-
Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, et al.Phylotranscriptomic analysis of the origin and early diversification of land plants. Proc Natl Acad Sci. 2014; 111(45):4859-868. doi: 10.1073/pnas.1323926111. http://www.pnas.org/content/111/45/E4859.full.pdf+html.
-
(2014)
Proc Natl Acad Sci
, vol.111
, Issue.45
, pp. 4859-4868
-
-
Wickett, N.J.1
Mirarab, S.2
Nguyen, N.3
Warnow, T.4
Carpenter, E.5
Matasci, N.6
-
10
-
-
84919947905
-
Coalescent versus concatenation methods and the placement of amborella as sister to water lilies
-
25077515 doi:10.1093/sysbio/syu055
-
Xi Z, Liu L, Rest JS, Davis CC. Coalescent versus concatenation methods and the placement of amborella as sister to water lilies. Syst Biol. 2014; 63(6):919-32. doi: 10.1093/sysbio/syu055. http://sysbio.oxfordjournals.org/content/63/6/919.full.pdf+html.
-
(2014)
Syst Biol
, vol.63
, Issue.6
, pp. 919-932
-
-
Xi, Z.1
Liu, L.2
Rest, J.S.3
Davis, C.C.4
-
11
-
-
84886742407
-
Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance
-
3874668 24180377 doi:10.1186/1748-7188-8-28. 1210.2665
-
Chaudhary R, Burleigh JG, Fernández-Baca D. Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance. Algorithms Mol Biol. 2013; 8:28. doi: 10.1186/1748-7188-8-28. 1210.2665
-
(2013)
Algorithms Mol Biol
, vol.8
, pp. 28
-
-
Chaudhary, R.1
Burleigh, J.G.2
Fernández-Baca, D.3
-
12
-
-
84910635621
-
Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal
-
25107551 doi:10.1093/molbev/msu235
-
Sharma PP, Kaluziak ST, Pérez-Porro AR, González VL, Hormiga G, Wheeler WC, et al.Phylogenomic interrogation of arachnida reveals systemic conflicts in phylogenetic signal. Mol Biol Evol. 2014; 31(11):2963-984. doi: 10.1093/molbev/msu235. http://mbe.oxfordjournals.org/content/31/11/2963.full.pdf+html.
-
(2014)
Mol Biol Evol
, vol.31
, Issue.11
, pp. 2963-2984
-
-
Sharma, P.P.1
Kaluziak, S.T.2
Pérez-Porro, A.R.3
González, V.L.4
Hormiga, G.5
Wheeler, W.C.6
-
13
-
-
57149095052
-
Dealing with incongruence in phylogenomic analyses
-
doi:10.1098/rstb.2008.0144
-
Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B: Biol Sci. 2008; 363(1512):4023-029. doi: 10.1098/rstb.2008.0144.
-
(2008)
Philos Trans R Soc Lond B: Biol Sci
, vol.363
, Issue.1512
, pp. 4023-4029
-
-
Galtier, N.1
Daubin, V.2
-
14
-
-
33846839390
-
Bayesian estimation of concordance among gene trees
-
17095535 doi:10.1093/molbev/msl170
-
Ané C, Larget B, Baum DA, Smith SD, Rokas A. Bayesian estimation of concordance among gene trees. Mol Biol Evol. 2007; 24:412-26. doi: 10.1093/molbev/msl170.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 412-426
-
-
Ané, C.1
Larget, B.2
Baum, D.A.3
Smith, S.D.4
Rokas, A.5
-
15
-
-
70450233546
-
Estimating species trees: Methods of phylogenetic analysis when there is incongruence across genes
-
20525600
-
Knowles LL. Estimating species trees: Methods of phylogenetic analysis when there is incongruence across genes. Syst Biol. 2009; 58(5):463-7.
-
(2009)
Syst Biol
, vol.58
, Issue.5
, pp. 463-467
-
-
Knowles, L.L.1
-
16
-
-
68049099068
-
Coalescent methods for estimating phylogenetic trees
-
1:CAS:528:DC%2BD1MXptlyktrw%3D 19501178 doi:10.1016/j.ympev.2009.05.033
-
Liu L, Yu L, Kubatko L, Pearl DK, Edwards SV. Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol. 2009; 53(1):320-8. doi: 10.1016/j.ympev.2009.05.033.
-
(2009)
Mol Phylogenet Evol
, vol.53
, Issue.1
, pp. 320-328
-
-
Liu, L.1
Yu, L.2
Kubatko, L.3
Pearl, D.K.4
Edwards, S.V.5
-
17
-
-
77958056150
-
Estimating species trees: An introduction to concepts and models
-
L.L. Knowles L.S. Kubatko, editors. Wiley-Blackwell Hoboken, New Jersey
-
Knowles LL, Kubatko LS. Estimating species trees: an introduction to concepts and models In: Knowles LL, Kubatko LS, editors. Estimating Species Trees: Practical and Theoretical Aspects. Hoboken, New Jersey: Wiley-Blackwell: 2010. p. 1-14.
-
(2010)
Estimating Species Trees: Practical and Theoretical Aspects
, pp. 1-14
-
-
Knowles, L.L.1
Kubatko, L.S.2
-
18
-
-
84866147332
-
Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy
-
22835380 doi:10.1016/j.ympev.2012.07.004
-
Knowles LL, Lanier HC, Klimov PB, He Q. Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy. Mol Phylogenet Evol. 2012; 65(2):501-9. doi: 10.1016/j.ympev.2012.07.004.
-
(2012)
Mol Phylogenet Evol
, vol.65
, Issue.2
, pp. 501-509
-
-
Knowles, L.L.1
Lanier, H.C.2
Klimov, P.B.3
He, Q.4
-
19
-
-
84917708481
-
Statistical binning enables an accurate coalescent-based estimation of the avian tree
-
Mirarab S, Bayzid MS, Boussau B, Warnow T. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science. 2014; 346(6215). doi: 10.1126/science.1250463. http://www.sciencemag.org/content/346/6215/1250463.full.pdf.
-
(2014)
Science
, vol.346
, Issue.6215
-
-
Mirarab, S.1
Bayzid, M.S.2
Boussau, B.3
Warnow, T.4
-
20
-
-
33846839295
-
Concordance trees, concordance factors, and the exploration of reticulate genealogy
-
Baum DA. Concordance trees, concordance factors, and the exploration of reticulate genealogy. Taxon. 2007; 56:417-26.
-
(2007)
Taxon
, vol.56
, pp. 417-426
-
-
Baum, D.A.1
-
21
-
-
78149256307
-
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
-
1:CAS:528:DC%2BC3cXhsVSlt7fE 20861028 doi:10.1093/bioinformatics/btq539
-
Larget BR, Kotha SK, Dewey CN, Ané C. BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics. 2010; 26:2910-911. doi: 10.1093/bioinformatics/btq539.
-
(2010)
Bioinformatics
, vol.26
, pp. 2910-2911
-
-
Larget, B.R.1
Kotha, S.K.2
Dewey, C.N.3
Ané, C.4
-
22
-
-
84883482283
-
Naive binning improves phylogenomic analyses
-
1:CAS:528:DC%2BC3sXhtlGmsLfM 23842808 doi:10.1093/bioinformatics/btt394
-
Bayzid MS, Warnow T. Naive binning improves phylogenomic analyses. Bioinformatics. 2013; 29:2277-284. doi: 10.1093/bioinformatics/btt394.
-
(2013)
Bioinformatics
, vol.29
, pp. 2277-2284
-
-
Bayzid, M.S.1
Warnow, T.2
-
23
-
-
84878113118
-
Inferring ancient divergences requires genes with strong phylogenetic signals
-
1:CAS:528:DC%2BC3sXnvFSjtLc%3D 23657258 doi:10.1038/nature12130
-
Salichos L, Rokas A. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature. 2013; 497:327-1. doi: 10.1038/nature12130.
-
(2013)
Nature
, vol.497
, pp. 327-331
-
-
Salichos, L.1
Rokas, A.2
-
24
-
-
84873326063
-
Genome-scale coestimation of species and gene trees
-
1:CAS:528:DC%2BC3sXitVemtL4%3D 3561873 23132911 doi:10.1101/gr.141978.112
-
Boussau B, Szollosi GJ, Duret L, Gouy M, Tannier E, Daubin V. Genome-scale coestimation of species and gene trees. Genome Res. 2013; 23:323-30. doi: 10.1101/gr.141978.112.
-
(2013)
Genome Res
, vol.23
, pp. 323-330
-
-
Boussau, B.1
Szollosi, G.J.2
Duret, L.3
Gouy, M.4
Tannier, E.5
Daubin, V.6
-
25
-
-
84898641369
-
Novel information theory-based measures for quantifying incongruence among phylogenetic trees
-
1:CAS:528:DC%2BC2cXmvFCitLs%3D 24509691 doi:10.1093/molbev/msu061
-
Salichos L, Stamatakis A, Rokas A. Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol Biol Evol. 2014; 31:1261-1271. doi: 10.1093/molbev/msu061.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 1261-1271
-
-
Salichos, L.1
Stamatakis, A.2
Rokas, A.3
-
26
-
-
84910656190
-
Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: Improving accuracy and matrix occupancy for phylogenomics
-
4209138 25158799 doi:10.1093/molbev/msu245
-
Yang Y, Smith SA. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: Improving accuracy and matrix occupancy for phylogenomics. Mol Biol Evol. 2014; 31:3081-092. doi: 10.1093/molbev/msu245.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 3081-3092
-
-
Yang, Y.1
Smith, S.A.2
-
27
-
-
84857090152
-
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses
-
Gorecki P, Burleigh GJ, Eulenstein O. Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinformatics. 2011; 12(Supp 1):1-15. doi: 10.1186/1471-2105-12-S1-S15.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 1-15
-
-
Gorecki, P.1
Burleigh, G.J.2
Eulenstein, O.3
-
28
-
-
84859546516
-
Unified modeling of gene duplication, loss, and coalescence using a locus tree
-
1:CAS:528:DC%2BC38Xlt1egtrg%3D 3317157 22271778 doi:10.1101/gr.123901.111
-
Rasmussen MD, Kellis M. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Res. 2012; 22(4):755-65. doi: 10.1101/gr.123901.111. http://genome.cshlp.org/content/22/4/755.full.pdf+html.
-
(2012)
Genome Res
, vol.22
, Issue.4
, pp. 755-765
-
-
Rasmussen, M.D.1
Kellis, M.2
-
29
-
-
84877597619
-
Optimizing de novo assembly of short-read RNA-seq data for phylogenomics
-
1:CAS:528:DC%2BC3sXptlyiurk%3D 3663818 23672450 doi:10.1186/1471-2164-14-328
-
Yang Y, Smith SA. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. BMC Genomics. 2013; 14:328. doi: 10.1186/1471-2164-14-328.
-
(2013)
BMC Genomics
, vol.14
, pp. 328
-
-
Yang, Y.1
Smith, S.A.2
-
30
-
-
84874372267
-
Family-level divergences in the stinging wasps (Hymenoptera: Aculeata), with correlations to angiosperm diversification
-
doi:10.1007/s11692-012-9189-0
-
Wilson JS, von Dohlen CD, Forister ML, Pitts JP. Family-level divergences in the stinging wasps (Hymenoptera: Aculeata), with correlations to angiosperm diversification. Evol Biol. 2013; 40:101-7. doi: 10.1007/s11692-012-9189-0.
-
(2013)
Evol Biol
, vol.40
, pp. 101-107
-
-
Wilson, J.S.1
Von Dohlen, C.D.2
Forister, M.L.3
Pitts, J.P.4
-
31
-
-
70350218974
-
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
-
doi:10.1111/j.1095-8339.2009.00996.x
-
Bremer B, Bremer K, Chase MW, Fay MF, Reveal JL, Bailey LH, et al.An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc. 2009; 161:105-21. doi: 10.1111/j.1095-8339.2009.00996.x.
-
(2009)
Bot J Linn Soc
, vol.161
, pp. 105-121
-
-
Bremer, B.1
Bremer, K.2
Chase, M.W.3
Fay, M.F.4
Reveal, J.L.5
Bailey, L.H.6
-
32
-
-
77955991477
-
The age and diversification of the angiosperms re-revisited
-
21616882 doi:10.3732/ajb.0900346
-
Bell CD, Soltis DE, Soltis PS. The age and diversification of the angiosperms re-revisited. Am J Bot. 2010; 97:1296-303. doi: 10.3732/ajb.0900346.
-
(2010)
Am J Bot
, vol.97
, pp. 1296-1303
-
-
Bell, C.D.1
Soltis, D.E.2
Soltis, P.S.3
-
33
-
-
77949494249
-
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots
-
1:CAS:528:DC%2BC3cXjs1emurc%3D 2842043 20176954 doi:10.1073/pnas.0907801107
-
Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE. Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci U S A. 2010; 107:4623-628. doi: 10.1073/pnas.0907801107.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 4623-4628
-
-
Moore, M.J.1
Soltis, P.S.2
Bell, C.D.3
Burleigh, J.G.4
Soltis, D.E.5
-
35
-
-
0036188663
-
Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences
-
21669721 doi:10.3732/ajb.89.1.132
-
Cuénoud P, Savolainen V, Chatrou LW, Powell M, Grayer RJ, Chase MW. Molecular phylogenetics of Caryophyllales based on nuclear 18S rDNA and plastid rbcL, atpB, and matK DNA sequences. Am J Bot. 2002; 89:132-44. doi: 10.3732/ajb.89.1.132.
-
(2002)
Am J Bot
, vol.89
, pp. 132-144
-
-
Cuénoud, P.1
Savolainen, V.2
Chatrou, L.W.3
Powell, M.4
Grayer, R.J.5
Chase, M.W.6
-
36
-
-
79955538408
-
Caryophyllales phylogenetics: Disentangling Phytolaccaceae and Molluginaceae and description of Microteaceae as a new isolated family
-
doi:10.3372/wi.39.39201
-
Schäferhoff B, Müller KF, Borsch T. Caryophyllales phylogenetics: disentangling Phytolaccaceae and Molluginaceae and description of Microteaceae as a new isolated family. Willdenowia. 2009; 39:209-28. doi: 10.3372/wi.39.39201.
-
(2009)
Willdenowia
, vol.39
, pp. 209-228
-
-
Schäferhoff, B.1
Müller, K.F.2
Borsch, T.3
-
37
-
-
79957676298
-
Contemporaneous and recent radiations of the world's major succulent plant lineages
-
1:CAS:528:DC%2BC3MXmsF2jt7k%3D 3100969 21536881 doi:10.1073/pnas.1100628108
-
Arakaki M, Christin PA, Nyffeler R, Lendel A, Eggli U, Ogburn RM, et al.Contemporaneous and recent radiations of the world's major succulent plant lineages. Proc Natl Acad Sci U S A. 2011; 108:8379-384. doi: 10.1073/pnas.1100628108.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 8379-8384
-
-
Arakaki, M.1
Christin, P.A.2
Nyffeler, R.3
Lendel, A.4
Eggli, U.5
Ogburn, R.M.6
-
38
-
-
70349169872
-
Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales
-
doi:10.1086/597785
-
Brockington SF, Alexandre R, Ramdial J, Moore MJ, Crawley S, Dhingra A, et al.Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales. Int J Plant Sci. 2009; 170:627-43. doi: 10.1086/597785.
-
(2009)
Int J Plant Sci
, vol.170
, pp. 627-643
-
-
Brockington, S.F.1
Alexandre, R.2
Ramdial, J.3
Moore, M.J.4
Crawley, S.5
Dhingra, A.6
-
39
-
-
79955778297
-
Complex pigment evolution in the Caryophyllales
-
1:CAS:528:DC%2BC3MXot1Crtbc%3D 21714182 doi:10.1111/j.1469-8137.2011.03687.x
-
Brockington SF, Walker RH, Glover BJ, Soltis PS, Soltis DE. Complex pigment evolution in the Caryophyllales. New Phytologist. 2011; 190:854-64. doi: 10.1111/j.1469-8137.2011.03687.x.
-
(2011)
New Phytologist
, vol.190
, pp. 854-864
-
-
Brockington, S.F.1
Walker, R.H.2
Glover, B.J.3
Soltis, P.S.4
Soltis, D.E.5
-
40
-
-
84863337944
-
Angiosperm phylogeny: 17 Genes, 640 taxa
-
21613169 doi:10.3732/ajb.1000404
-
Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, et al.Angiosperm phylogeny: 17 genes, 640 taxa. Am J Bot. 2011; 98:704-30. doi: 10.3732/ajb.1000404.
-
(2011)
Am J Bot
, vol.98
, pp. 704-730
-
-
Soltis, D.E.1
Smith, S.A.2
Cellinese, N.3
Wurdack, K.J.4
Tank, D.C.5
Brockington, S.F.6
-
41
-
-
84856214128
-
Impact of missing data, gene choice, and taxon sampling on phylogenetic reconstruction: The Caryophyllales (angiosperms)
-
doi:10.1007/s00606-011-0544-x
-
Crawley SS, Hilu KW. Impact of missing data, gene choice, and taxon sampling on phylogenetic reconstruction: The Caryophyllales (angiosperms). Plant Syst Evol. 2012; 298:297-312. doi: 10.1007/s00606-011-0544-x.
-
(2012)
Plant Syst Evol
, vol.298
, pp. 297-312
-
-
Crawley, S.S.1
Hilu, K.W.2
-
42
-
-
84965099240
-
Dissecting molecular evolution in the highly diverse plant clade caryophyllales using transcriptome sequencing
-
Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK-S, Carpenter EJ, et al.Dissecting molecular evolution in the highly diverse plant clade caryophyllales using transcriptome sequencing. Mol Biol Evol. 2015. doi: 10.1093/molbev/msv081. http://mbe.oxfordjournals.org/content/early/2015/04/22/molbev.msv081.full.pdf+html.
-
(2015)
Mol Biol Evol
-
-
Yang, Y.1
Moore, M.J.2
Brockington, S.F.3
Soltis, D.E.4
Wong, G.K.-S.5
Carpenter, E.J.6
-
43
-
-
33750460281
-
Insights into social insects from the genome of the honeybee Apis mellifera
-
1:CAS:528:DC%2BD28XhtFaksrjK doi:10.1038/nature05260
-
Weinstock GM, Robinson GE, Gibbs RA, Worley KC, Evans JD, Maleszka R, et al.Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006; 443:931-49. doi: 10.1038/nature05260.
-
(2006)
Nature
, vol.443
, pp. 931-949
-
-
Weinstock, G.M.1
Robinson, G.E.2
Gibbs, R.A.3
Worley, K.C.4
Evans, J.D.5
Maleszka, R.6
-
44
-
-
77956109363
-
Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator
-
1:CAS:528:DC%2BC3cXhtVGrt7bF 3772619 20798317 doi:10.1126/science.1192428
-
Bonasio R, Zhang G, Ye C, Mutti NS, Fang X, Qin N, et al.Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator. Science. 2010; 329:1068-71. doi: 10.1126/science.1192428.
-
(2010)
Science
, vol.329
, pp. 1068-1071
-
-
Bonasio, R.1
Zhang, G.2
Ye, C.3
Mutti, N.S.4
Fang, X.5
Qin, N.6
-
45
-
-
74549184089
-
The Nasonia Genome Working Group: Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
-
1:CAS:528:DC%2BC3cXktlWlug%3D%3D 20075255 doi:10.1126/science.1178028
-
Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK. The Nasonia Genome Working Group: Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science. 2010; 327:343-8. doi: 10.1126/science.1178028.
-
(2010)
Science
, vol.327
, pp. 343-348
-
-
Werren, J.H.1
Richards, S.2
Desjardins, C.A.3
Niehuis, O.4
Gadau, J.5
Colbourne, J.K.6
-
46
-
-
79955002712
-
Draft genome of the red harvester ant Pogonomyrmex barbatus
-
1:CAS:528:DC%2BC3MXkvVCjt7s%3D 3078412 21282651 doi:10.1073/pnas.1007901108
-
Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, et al.Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci U S A. 2011; 108:5667-672. doi: 10.1073/pnas.1007901108.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 5667-5672
-
-
Smith, C.R.1
Smith, C.D.2
Robertson, H.M.3
Helmkampf, M.4
Zimin, A.5
Yandell, M.6
-
47
-
-
79954986915
-
Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)
-
1:CAS:528:DC%2BC3MXkvVCju7s%3D 3078359 21282631 doi:10.1073/pnas.1008617108
-
Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, et al.Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci U S A. 2011; 108:5673-678. doi: 10.1073/pnas.1008617108.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 5673-5678
-
-
Smith, C.D.1
Zimin, A.2
Holt, C.3
Abouheif, E.4
Benton, R.5
Cash, E.6
-
48
-
-
84890455442
-
The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes
-
doi:10.1186/gb-2013-14-12-r142
-
Kocher SD, Li C, Yang W, Tan H, Yi SV, Yang X, et al.The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biol. 2013; 14:142. doi: 10.1186/gb-2013-14-12-r142.
-
(2013)
Genome Biol
, vol.14
, pp. 142
-
-
Kocher, S.D.1
Li, C.2
Yang, W.3
Tan, H.4
Yi, S.V.5
Yang, X.6
-
49
-
-
84938673045
-
-
PhD thesis, University of Utrecht
-
van Dongen S. Graph clustering: PhD thesis, University of Utrecht; 2000.
-
(2000)
Graph Clustering
-
-
Van Dongen, S.1
-
50
-
-
84875619226
-
MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
-
1:CAS:528:DC%2BC3sXksFWisLc%3D 3603318 23329690 doi:10.1093/molbev/mst010
-
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol. 2013; 30:772-80. doi: 10.1093/molbev/mst010.
-
(2013)
Mol Biol Evol
, vol.30
, pp. 772-780
-
-
Katoh, K.1
Standley, D.M.2
-
51
-
-
84555194934
-
SATe-II: Very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees
-
22139466 doi:10.1093/sysbio/syr095
-
Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, et al.SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst Biol. 2012; 61:90-106. doi: 10.1093/sysbio/syr095.
-
(2012)
Syst Biol
, vol.61
, pp. 90-106
-
-
Liu, K.1
Warnow, T.J.2
Holder, M.T.3
Nelesen, S.M.4
Yu, J.5
Stamatakis, A.P.6
-
52
-
-
84899553363
-
RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
-
1:CAS:528:DC%2BC2cXmvFCjsbc%3D 3998144 24451623 doi:10.1093/bioinformatics/btu033 bioinformatics/btu033
-
Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30:1312-1313. doi: 10.1093/bioinformatics/btu033 bioinformatics/btu033
-
(2014)
Bioinformatics
, vol.30
, pp. 1312-1313
-
-
Stamatakis, A.1
-
53
-
-
65649131928
-
Gene tree discordance, phylogenetic inference and the multispecies coalescent
-
19307040 doi:10.1016/j.tree.2009.01.009
-
Degnan JH, Rosenberg NA. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol Evol. 2009; 24:332-40. doi: 10.1016/j.tree.2009.01.009.
-
(2009)
Trends Ecol Evol
, vol.24
, pp. 332-340
-
-
Degnan, J.H.1
Rosenberg, N.A.2
-
54
-
-
13244292527
-
Gene tree distributions under the coalescent process
-
15792224 doi:10.1111/j.0014-3820.2005.tb00891.x
-
Degnan JH, Salter LA. Gene tree distributions under the coalescent process. Evolution. 2005; 59(1):24-37. doi: 10.1111/j.0014-3820.2005.tb00891.x.
-
(2005)
Evolution
, vol.59
, Issue.1
, pp. 24-37
-
-
Degnan, J.H.1
Salter, L.A.2
-
55
-
-
84870458929
-
treepl: Divergence time estimation using penalized likelihood for large phylogenies
-
1:CAS:528:DC%2BC38XhsFWktrrO 22908216 doi:10.1093/bioinformatics/bts492
-
Smith SA, O'Meara BC. treepl: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics. 2012; 28(20):2689-690. doi: 10.1093/bioinformatics/bts492. http://bioinformatics.oxfordjournals.org/content/28/20/2689.full.pdf+html.
-
(2012)
Bioinformatics
, vol.28
, Issue.20
, pp. 2689-2690
-
-
Smith, S.A.1
O'Meara, B.C.2
-
56
-
-
3042672020
-
Functional annotation of the Arabidopsis genome using controlled vocabularies
-
1:CAS:528:DC%2BD2cXltlKjurg%3D 514112 15173566 doi:10.1104/pp.104.040071
-
Berardini TZ, Mundodi S, Reiser L, Huala E, Garcia-Hernandez M, Zhang P, et al.Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol. 2004; 135:745-55. doi: 10.1104/pp.104.040071.
-
(2004)
Plant Physiol
, vol.135
, pp. 745-755
-
-
Berardini, T.Z.1
Mundodi, S.2
Reiser, L.3
Huala, E.4
Garcia-Hernandez, M.5
Zhang, P.6
-
57
-
-
84891808813
-
FlyBase 102-advanced approaches to interrogating FlyBase
-
doi:10.1093/nar/gkt1092
-
St Pierre SE, Ponting L, Stefancsik R, McQuilton P. FlyBase 102-advanced approaches to interrogating FlyBase. Nucleic Acids Res. 2014; 42:780-8. doi: 10.1093/nar/gkt1092.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. 780-788
-
-
St Pierre, S.E.1
Ponting, L.2
Stefancsik, R.3
McQuilton, P.4
-
58
-
-
51349098340
-
Phylonet: A software package for analyzing and reconstructing reticulate evolutionary relationships
-
2533029 18662388 doi:10.1186/1471-2105-9-322
-
Than C, Ruths D, Nakhleh L. Phylonet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics. 2008; 9(1):322. doi: 10.1186/1471-2105-9-322.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.1
, pp. 322
-
-
Than, C.1
Ruths, D.2
Nakhleh, L.3
-
59
-
-
70349425459
-
Estimating species phylogenies using coalescence times among sequences
-
1:CAS:528:DC%2BD1MXhsVCisbjN 20525601 doi:10.1093/sysbio/syp031
-
Liu L, Yu L, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Syst Biol. 2009; 58(5):468-77. doi: 10.1093/sysbio/syp031. http://sysbio.oxfordjournals.org/content/58/5/468.full.pdf+html.
-
(2009)
Syst Biol
, vol.58
, Issue.5
, pp. 468-477
-
-
Liu, L.1
Yu, L.2
Pearl, D.K.3
Edwards, S.V.4
-
60
-
-
84922482181
-
Extensive introgression in a malaria vector species complex revealed by phylogenomics
-
Fontaine MC, Pease JB, Steele A, Waterhouse RM, Neafsey DE, Sharakhov IV, et al.Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science. 6217; 347. doi: 10.1126/science.1258524. http://www.sciencemag.org/content/347/6217/1258524.full.pdf.
-
Science
, vol.6217
, pp. 347
-
-
Fontaine, M.C.1
Pease, J.B.2
Steele, A.3
Waterhouse, R.M.4
Neafsey, D.E.5
Sharakhov, I.V.6
-
61
-
-
84906251283
-
Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3
-
1:CAS:528:DC%2BC2cXhtl2gur3P 24721692 doi:10.1093/sysbio/syu027
-
Zwickl DJ, Stein JC, Wing RA, Ware D, Sanderson MJ. Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3. Syst Biol. 2014; 63:645-59. doi: 10.1093/sysbio/syu027.
-
(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
|