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Items: 1 to 20 of 102

1.

A phylogenomics approach for selecting robust sets of phylogenetic markers.

Capella-Gutierrez S, Kauff F, Gabaldón T.

Nucleic Acids Res. 2014 Apr;42(7):e54. doi: 10.1093/nar/gku071. Epub 2014 Jan 29.

2.

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.

Fitzpatrick DA, Logue ME, Stajich JE, Butler G.

BMC Evol Biol. 2006 Nov 22;6:99.

3.

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
4.

New molecular markers for fungal phylogenetics: two genes for species-level systematics in the Sordariomycetes (Ascomycota).

Walker DM, Castlebury LA, Rossman AY, White JF Jr.

Mol Phylogenet Evol. 2012 Sep;64(3):500-12. doi: 10.1016/j.ympev.2012.05.005. Epub 2012 May 22.

PMID:
22626621
5.
6.

A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher level relationships of the caudata.

Shen XX, Liang D, Feng YJ, Chen MY, Zhang P.

Mol Biol Evol. 2013 Oct;30(10):2235-48. doi: 10.1093/molbev/mst122. Epub 2013 Jul 4.

PMID:
23827877
7.
8.

Multilocus phylogeny of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota): insights on diversity, distributions, and a comparison of species tree and concatenated topologies.

Leavitt SD, Esslinger TL, Spribille T, Divakar PK, Thorsten Lumbsch H.

Mol Phylogenet Evol. 2013 Jan;66(1):138-52. doi: 10.1016/j.ympev.2012.09.013. Epub 2012 Sep 24.

PMID:
23017822
9.

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.

Miadlikowska J, Kauff F, Högnabba F, Oliver JC, Molnár K, Fraker E, Gaya E, Hafellner J, Hofstetter V, Gueidan C, Otálora MA, Hodkinson B, Kukwa M, Lücking R, Björk C, Sipman HJ, Burgaz AR, Thell A, Passo A, Myllys L, Goward T, Fernández-Brime S, Hestmark G, Lendemer J, Lumbsch HT, Schmull M, Schoch CL, Sérusiaux E, Maddison DR, Arnold AE, Lutzoni F, Stenroos S.

Mol Phylogenet Evol. 2014 Oct;79:132-68. doi: 10.1016/j.ympev.2014.04.003. Epub 2014 Apr 18.

10.

Lactobacillus phylogenomics--towards a reclassification of the genus.

Claesson MJ, van Sinderen D, O'Toole PW.

Int J Syst Evol Microbiol. 2008 Dec;58(Pt 12):2945-54. doi: 10.1099/ijs.0.65848-0.

PMID:
19060088
11.

Integrating Markov clustering and molecular phylogenetics to reconstruct the cyanobacterial species tree from conserved protein families.

Swingley WD, Blankenship RE, Raymond J.

Mol Biol Evol. 2008 Apr;25(4):643-54. doi: 10.1093/molbev/msn034. Epub 2008 Feb 22.

PMID:
18296704
12.

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.

13.

Evolutionary relationships of the cup-fungus genus Peziza and Pezizaceae inferred from multiple nuclear genes: RPB2, beta-tubulin, and LSU rDNA.

Hansen K, Lobuglio KF, Pfister DH.

Mol Phylogenet Evol. 2005 Jul;36(1):1-23. Epub 2005 Apr 22.

PMID:
15904853
14.

Phylogenomics and the reconstruction of the tree of life.

Delsuc F, Brinkmann H, Philippe H.

Nat Rev Genet. 2005 May;6(5):361-75. Review.

15.

Genome-scale approaches to resolving incongruence in molecular phylogenies.

Rokas A, Williams BL, King N, Carroll SB.

Nature. 2003 Oct 23;425(6960):798-804.

16.
17.

Different phylogenomic approaches to resolve the evolutionary relationships among model fish species.

Negrisolo E, Kuhl H, Forcato C, Vitulo N, Reinhardt R, Patarnello T, Bargelloni L.

Mol Biol Evol. 2010 Dec;27(12):2757-74. doi: 10.1093/molbev/msq165. Epub 2010 Jun 29.

PMID:
20591844
18.

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.

McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC.

Genome Res. 2012 Apr;22(4):746-54. doi: 10.1101/gr.125864.111. Epub 2011 Dec 29.

19.

Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis.

de Vienne DM, Ollier S, Aguileta G.

Mol Biol Evol. 2012 Jun;29(6):1587-98. doi: 10.1093/molbev/msr317. Epub 2012 Jan 3.

PMID:
22319162
20.

Phylogenomics: evolution and genomics intersection.

Gomase VS, Tagore S.

Int J Bioinform Res Appl. 2009;5(5):548-63.

PMID:
19778869

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