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Rooting the eutherian tree: the power and pitfalls of phylogenomics
Hidenori Nishihara, Norihiro Okada, Masami Hasegawa
Genome Biol. 2007; 8(9): R199. Published online 2007 September 21. doi: 10.1186/gb-2007-8-9-r199
PMCID:
PMC2375037
Abstract Full Text PDF–338K Supplementary Material

Is Cited by the Following 17 Articles in this Archive:

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
John E. McCormack, Brant C. Faircloth, Nicholas G. Crawford, Patricia Adair Gowaty, Robb T. Brumfield, Travis C. Glenn
Genome Res. 2012 April; 22(4): 746–754. doi: 10.1101/gr.125864.111
PMCID:
PMC3317156
Free in PMC on 2012/10/01
A Comparative Study of Mammalian Diversification Pattern
Wenhua Yu, Junxiao Xu, Yi Wu, Guang Yang
Int J Biol Sci. 2012; 8(4): 486–497. Published online 2012 March 14. doi: 10.7150/ijbs.3982
PMCID:
PMC3314190
Abstract Full Text PDF–977K
Statistics and Truth in Phylogenomics
Sudhir Kumar, Alan J. Filipski, Fabia U. Battistuzzi, Sergei L. Kosakovsky Pond, Koichiro Tamura
Mol Biol Evol. 2012 February; 29(2): 457–472. Published online 2011 August 26. doi: 10.1093/molbev/msr202
PMCID:
PMC3258035
Free in PMC on 2013/02/01
Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited
Jaqueline Hess, Nick Goldman
PLoS One. 2011; 6(8): e22783. Published online 2011 August 5. doi: 10.1371/journal.pone.0022783
PMCID:
PMC3151265
Abstract Full Text PDF–1.0M Supplementary Material
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
Hervé Philippe, Henner Brinkmann, Dennis V. Lavrov, D. Timothy J. Littlewood, Michael Manuel, Gert Wörheide, Denis Baurain
PLoS Biol. 2011 March; 9(3): e1000602. Published online 2011 March 15. doi: 10.1371/journal.pbio.1000602
PMCID:
PMC3057953
Full Text PDF–468K Supplementary Material
The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis
Véronique Campbell, Pierre Legendre, François-Joseph Lapointe
BMC Evol Biol. 2011; 11: 64. Published online 2011 March 9. doi: 10.1186/1471-2148-11-64
PMCID:
PMC3065422
Abstract Full Text PDF–470K
Mammalian Evolution May not Be Strictly Bifurcating
Björn M. Hallström, Axel Janke
Mol Biol Evol. 2010 December; 27(12): 2804–2816. Published online 2010 June 29. doi: 10.1093/molbev/msq166
PMCID:
PMC2981514
Abstract Full Text PDF–493K Supplementary Material
An Application of Supertree Methods to Mammalian Mitogenomic Sequences
Véronique Campbell, François-Joseph Lapointe
Evol Bioinform Online. 2010; 6: 57–71. Published online 2010 May 12.
PMCID:
PMC2880846
Abstract Full Text PDF–675K
Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees
Patrick Kück, Karen Meusemann, Johannes Dambach, Birthe Thormann, Björn M von Reumont, Johann W Wägele, Bernhard Misof
Front Zool. 2010; 7: 10. Published online 2010 March 31. doi: 10.1186/1742-9994-7-10
PMCID:
PMC2867768
Abstract Full Text PDF–876K Supplementary Material
Mosaic retroposon insertion patterns in placental mammals
Gennady Churakov, Jan Ole Kriegs, Robert Baertsch, Anja Zemann, Jürgen Brosius, Jürgen Schmitz
Genome Res. 2009 May; 19(5): 868–875. doi: 10.1101/gr.090647.108
PMCID:
PMC2675975
Abstract Full Text PDF–1.4M
Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals
Hidenori Nishihara, Shigenori Maruyama, Norihiro Okada
Proc Natl Acad Sci U S A. 2009 March 31; 106(13): 5235–5240. Published online 2009 March 13. doi: 10.1073/pnas.0809297106
PMCID:
PMC2655268
Abstract Full Text PDF–437K Supplementary Material
The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees
Chih-Horng Kuo, John P. Wares, Jessica C. Kissinger
Mol Biol Evol. 2008 December; 25(12): 2689–2698. Published online 2008 September 26. doi: 10.1093/molbev/msn213
PMCID:
PMC2582981
Abstract Full Text PDF–131K Supplementary Material
Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations
Björn M Hallström, Axel Janke
BMC Evol Biol. 2008; 8: 162. Published online 2008 May 27. doi: 10.1186/1471-2148-8-162
PMCID:
PMC2435553
Abstract Full Text PDF–343K
Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets
Arjun B. Prasad, Marc W. Allard, Eric D. Green, NISC Comparative Sequencing Program
Mol Biol Evol. 2008 September; 25(9): 1795–1808. Published online 2008 May 2. doi: 10.1093/molbev/msn104
PMCID:
PMC2515873
Abstract Full Text PDF–589K Supplementary Material
Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods
Stéphane Aris-Brosou, Xuhua Xia
Int J Plant Genomics. 2008; 2008: 683509. Published online 2008 April 30. doi: 10.1155/2008/683509
PMCID:
PMC2375977
Abstract Full Text PDF–656K
Analysis of 142 genes resolves the rapid diversification of the rice genus
Xin-Hui Zou, Fu-Min Zhang, Jian-Guo Zhang, Li-Li Zang, Liang Tang, Jun Wang, Tao Sang, Song Ge
Genome Biol. 2008; 9(3): R49. Published online 2008 March 3. doi: 10.1186/gb-2008-9-3-r49
PMCID:
PMC2397501
Abstract Full Text PDF–466K Supplementary Material
OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics
Vincent Ranwez, Frédéric Delsuc, Sylvie Ranwez, Khalid Belkhir, Marie-Ka Tilak, Emmanuel JP Douzery
BMC Evol Biol. 2007; 7: 241. Published online 2007 November 30. doi: 10.1186/1471-2148-7-241
PMCID:
PMC2249597
Abstract Full Text PDF–1.1M
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