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Items: 1 to 20 of 33

1.

Large-scale assignment of orthology: back to phylogenetics?

Gabaldón T.

Genome Biol. 2008 Oct 30;9(10):235. doi: 10.1186/gb-2008-9-10-235. Review.

2.

Alignment uncertainty and genomic analysis.

Wong KM, Suchard MA, Huelsenbeck JP.

Science. 2008 Jan 25;319(5862):473-6. doi: 10.1126/science.1151532.

3.

TreeFam: 2008 Update.

Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Hériché JK, Hu Y, Kristiansen K, Li R, Liu T, Moses A, Qin J, Vang S, Vilella AJ, Ureta-Vidal A, Bolund L, Wang J, Durbin R.

Nucleic Acids Res. 2008 Jan;36(Database issue):D735-40. Epub 2007 Dec 1.

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Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi.

Cornell MJ, Alam I, Soanes DM, Wong HM, Hedeler C, Paton NW, Rattray M, Hubbard SJ, Talbot NJ, Oliver SG.

Genome Res. 2007 Dec;17(12):1809-22. Epub 2007 Nov 5.

6.

PhylomeDB: a database for genome-wide collections of gene phylogenies.

Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6. Epub 2007 Oct 25.

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The human phylome.

Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T.

Genome Biol. 2007;8(6):R109.

10.

Supertrees disentangle the chimerical origin of eukaryotic genomes.

Pisani D, Cotton JA, McInerney JO.

Mol Biol Evol. 2007 Aug;24(8):1752-60. Epub 2007 May 15.

11.

High-resolution species trees without concatenation.

Edwards SV, Liu L, Pearl DK.

Proc Natl Acad Sci U S A. 2007 Apr 3;104(14):5936-41. Epub 2007 Mar 28.

12.

Orthology prediction at scalable resolution by phylogenetic tree analysis.

van der Heijden RT, Snel B, van Noort V, Huynen MA.

BMC Bioinformatics. 2007 Mar 8;8:83.

13.

Assessment of phylogenomic and orthology approaches for phylogenetic inference.

Dutilh BE, van Noort V, van der Heijden RT, Boekhout T, Snel B, Huynen MA.

Bioinformatics. 2007 Apr 1;23(7):815-24. Epub 2007 Jan 19.

14.

Phylogenomics reveal a robust fungal tree of life.

Kuramae EE, Robert V, Snel B, Weiss M, Boekhout T.

FEMS Yeast Res. 2006 Dec;6(8):1213-20.

15.

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.

16.

Bayesian estimation of concordance among gene trees.

Ané C, Larget B, Baum DA, Smith SD, Rokas A.

Mol Biol Evol. 2007 Feb;24(2):412-26. Epub 2006 Nov 9. Erratum in: Mol Biol Evol. 2007 Jul;24(7):1575.

17.

The tree of one percent.

Dagan T, Martin W.

Genome Biol. 2006;7(10):118. Epub 2006 Nov 1.

18.

Optimal gene trees from sequences and species trees using a soft interpretation of parsimony.

Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA.

J Mol Evol. 2006 Aug;63(2):240-50. Epub 2006 Jul 7.

PMID:
16830091
19.

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.

Anisimova M, Gascuel O.

Syst Biol. 2006 Aug;55(4):539-52.

PMID:
16785212
20.

A phylogenomic analysis of the Ascomycota.

Robbertse B, Reeves JB, Schoch CL, Spatafora JW.

Fungal Genet Biol. 2006 Oct;43(10):715-25. Epub 2006 Jun 15.

PMID:
16781175
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