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SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics.

Roure B, Rodriguez-Ezpeleta N, Philippe H.

BMC Evol Biol. 2007 Feb 8;7 Suppl 1:S2.PMID: 17288575 [PubMed - indexed for MEDLINE]Related articlesFree article

TaxMan: a taxonomic database manager.

Jones M, Blaxter M.

BMC Bioinformatics. 2006 Dec 18;7:536.PMID: 17176465 [PubMed - indexed for MEDLINE]Related articlesFree article

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219.PMID: 19607672 [PubMed - indexed for MEDLINE]Related articlesFree article

PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences.

Hanekamp K, Bohnebeck U, Beszteri B, Valentin K.

Bioinformatics. 2007 Apr 1;23(7):793-801. Epub 2007 Mar 1.PMID: 17332025 [PubMed - indexed for MEDLINE]Related articlesFree article

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Hartmann S, Vision TJ.

BMC Evol Biol. 2008 Mar 26;8:95.PMID: 18366758 [PubMed - indexed for MEDLINE]Related articlesFree article

From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case.

Comas I, Moya A, González-Candelas F.

Syst Biol. 2007 Feb;56(1):1-16.PMID: 17366133 [PubMed - indexed for MEDLINE]Related articles

RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits.

Teeling H, Gloeckner FO.

BMC Bioinformatics. 2006 Feb 13;7:66.PMID: 16476165 [PubMed - indexed for MEDLINE]Related articlesFree article

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.

Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H.

Syst Biol. 2005 Oct;54(5):743-57.PMID: 16243762 [PubMed - indexed for MEDLINE]Related articles

Rooting the eutherian tree: the power and pitfalls of phylogenomics.

Nishihara H, Okada N, Hasegawa M.

Genome Biol. 2007;8(9):R199.PMID: 17883877 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 17237036 [PubMed - indexed for MEDLINE]Related articlesFree article

TaxI: a software tool for DNA barcoding using distance methods.

Steinke D, Vences M, Salzburger W, Meyer A.

Philos Trans R Soc Lond B Biol Sci. 2005 Oct 29;360(1462):1975-80.PMID: 16214755 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.PMID: 16729895 [PubMed - indexed for MEDLINE]Related articlesFree article

Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny.

Russo CA, Takezaki N, Nei M.

Mol Biol Evol. 1996 Mar;13(3):525-36.PMID: 8742641 [PubMed - indexed for MEDLINE]Related articlesFree article

Tracing evolutionary pressure.

Ye K, Vriend G, IJzerman AP.

Bioinformatics. 2008 Apr 1;24(7):908-15. Epub 2008 Feb 26.PMID: 18304936 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploration of phylogenetic data using a global sequence analysis method.

Chapus C, Dufraigne C, Edwards S, Giron A, Fertil B, Deschavanne P.

BMC Evol Biol. 2005 Nov 9;5:63.PMID: 16280081 [PubMed - indexed for MEDLINE]Related articlesFree article

Evolution and trans-species polymorphism of MHC class IIbeta genes in cyprinid fish.

Ottová E, Simková A, Martin JF, de Bellocq JG, Gelnar M, Allienne JF, Morand S.

Fish Shellfish Immunol. 2005 Mar;18(3):199-222.PMID: 15519540 [PubMed - indexed for MEDLINE]Related articles

BranchClust: a phylogenetic algorithm for selecting gene families.

Poptsova MS, Gogarten JP.

BMC Bioinformatics. 2007 Apr 10;8:120.PMID: 17425803 [PubMed - indexed for MEDLINE]Related articlesFree article

An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences.

Brochier C, Forterre P, Gribaldo S.

BMC Evol Biol. 2005 Jun 2;5(1):36.PMID: 15932645 [PubMed - indexed for MEDLINE]Related articlesFree article

Taxonomic colouring of phylogenetic trees of protein sequences.

Palidwor G, Reynaud EG, Andrade-Navarro MA.

BMC Bioinformatics. 2006 Feb 17;7:79.PMID: 16503967 [PubMed - indexed for MEDLINE]Related articlesFree article

Fast NJ-like algorithms to deal with incomplete distance matrices.

Criscuolo A, Gascuel O.

BMC Bioinformatics. 2008 Mar 26;9:166.PMID: 18366787 [PubMed - indexed for MEDLINE]Related articlesFree article