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Items: 1 to 20 of 123

1.

Factors affecting the concordance between orthologous gene trees and species tree in bacteria.

Castillo-Ramírez S, González V.

BMC Evol Biol. 2008 Oct 30;8:300. doi: 10.1186/1471-2148-8-300.

2.

Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.

3.

Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design.

McCormack JE, Huang H, Knowles LL.

Syst Biol. 2009 Oct;58(5):501-8. doi: 10.1093/sysbio/syp045. Epub 2009 Aug 20.

PMID:
20525604
4.

Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer.

Chung Y, Ané C.

Syst Biol. 2011 May;60(3):261-75. doi: 10.1093/sysbio/syr003. Epub 2011 Mar 2.

PMID:
21368324
6.

The probability of topological concordance of gene trees and species trees.

Rosenberg NA.

Theor Popul Biol. 2002 Mar;61(2):225-47.

PMID:
11969392
8.

Discordance of species trees with their most likely gene trees: a unifying principle.

Rosenberg NA.

Mol Biol Evol. 2013 Dec;30(12):2709-13. doi: 10.1093/molbev/mst160. Epub 2013 Sep 12.

9.

Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract.

Nicolas P, Bessières P, Ehrlich SD, Maguin E, van de Guchte M.

BMC Evol Biol. 2007 Aug 20;7:141.

10.

What is the danger of the anomaly zone for empirical phylogenetics?

Huang H, Knowles LL.

Syst Biol. 2009 Oct;58(5):527-36. doi: 10.1093/sysbio/syp047. Epub 2009 Aug 26.

PMID:
20525606
12.

Discordance of species trees with their most likely gene trees.

Degnan JH, Rosenberg NA.

PLoS Genet. 2006 May;2(5):e68. Epub 2006 May 26.

13.

Comparison of methods for species-tree inference in the sawfly genus Neodiprion (Hymenoptera: Diprionidae).

Linnen CR, Farrell BD.

Syst Biol. 2008 Dec;57(6):876-90. doi: 10.1080/10635150802580949.

PMID:
19085330
14.

Does a tree-like phylogeny only exist at the tips in the prokaryotes?

Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO.

Proc Biol Sci. 2004 Dec 22;271(1557):2551-8.

15.

A multilocus phylogeny of the Sulidae (Aves: Pelecaniformes).

Patterson SA, Morris-Pocock JA, Friesen VL.

Mol Phylogenet Evol. 2011 Feb;58(2):181-91. doi: 10.1016/j.ympev.2010.11.021. Epub 2010 Dec 7.

PMID:
21144905
16.

Detecting phylogenetic breakpoints and discordance from genome-wide alignments for species tree reconstruction.

Ané C.

Genome Biol Evol. 2011;3:246-58. doi: 10.1093/gbe/evr013. Epub 2011 Feb 28.

17.

Species tree estimation for a deep phylogenetic divergence in the New World monkeys (Primates: Platyrrhini).

Perez SI, Klaczko J, dos Reis SF.

Mol Phylogenet Evol. 2012 Nov;65(2):621-30. doi: 10.1016/j.ympev.2012.07.014. Epub 2012 Jul 24.

PMID:
22841656
18.

Assessing the performance of single-copy genes for recovering robust phylogenies.

Aguileta G, Marthey S, Chiapello H, Lebrun MH, Rodolphe F, Fournier E, Gendrault-Jacquemard A, Giraud T.

Syst Biol. 2008 Aug;57(4):613-27. doi: 10.1080/10635150802306527.

PMID:
18709599
19.

Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods.

Huang H, He Q, Kubatko LS, Knowles LL.

Syst Biol. 2010 Oct;59(5):573-83. doi: 10.1093/sysbio/syq047. Epub 2010 Sep 10.

PMID:
20833951
20.

Multiple consensus trees: a method to separate divergent genes.

Guénoche A.

BMC Bioinformatics. 2013 Feb 9;14:46. doi: 10.1186/1471-2105-14-46.

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