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Large-scale assignment of orthology: back to phylogenetics?

Gabaldón T.

Genome Biol. 2008 Oct 30;9(10):235.PMID: 18983710 [PubMed - in process]Related articlesFree article

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits.

Dessimoz C, Boeckmann B, Roth AC, Gonnet GH.

Nucleic Acids Res. 2006 Jul 11;34(11):3309-16. Print 2006.PMID: 16835308 [PubMed - indexed for MEDLINE]Related articlesFree article

OrthologID: automation of genome-scale ortholog identification within a parsimony framework.

Chiu JC, Lee EK, Egan MG, Sarkar IN, Coruzzi GM, DeSalle R.

Bioinformatics. 2006 Mar 15;22(6):699-707. Epub 2006 Jan 12.PMID: 16410324 [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

Phylogenetic and functional assessment of orthologs inference projects and methods.

Altenhoff AM, Dessimoz C.

PLoS Comput Biol. 2009 Jan;5(1):e1000262. Epub 2009 Jan 16.PMID: 19148271 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 17346331 [PubMed - indexed for MEDLINE]Related articlesFree article

Animal phylogenomics: multiple interspecific genome comparisons.

DeSalle R.

Methods Enzymol. 2005;395:104-33.PMID: 15865964 [PubMed - indexed for MEDLINE]Related articles

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.

Storm CE, Sonnhammer EL.

Bioinformatics. 2002 Jan;18(1):92-9.PMID: 11836216 [PubMed - indexed for MEDLINE]Related articlesFree article

[Foundations of the new phylogenetics]

Pavlinov IIa.

Zh Obshch Biol. 2004 Jul-Aug;65(4):334-66. Russian. PMID: 15490579 [PubMed - indexed for MEDLINE]Related articles

Gene family evolution and homology: genomics meets phylogenetics.

Thornton JW, DeSalle R.

Annu Rev Genomics Hum Genet. 2000;1:41-73. Review.PMID: 11701624 [PubMed - indexed for MEDLINE]Related articles

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R.

PLoS One. 2009 Jun 2;4(6):e5764.PMID: 19503618 [PubMed - indexed for MEDLINE]Related articlesFree article

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

Arvestad L, Berglund AC, Lagergren J, Sennblad B.

Bioinformatics. 2003;19 Suppl 1:i7-15.PMID: 12855432 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogenetic reconstruction of orthology, paralogy, and conserved synteny for dog and human.

Goodstadt L, Ponting CP.

PLoS Comput Biol. 2006 Sep 29;2(9):e133.PMID: 17009864 [PubMed - indexed for MEDLINE]Related articlesFree article

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Remm M, Storm CE, Sonnhammer EL.

J Mol Biol. 2001 Dec 14;314(5):1041-52.PMID: 11743721 [PubMed - indexed for MEDLINE]Related articles

HaMStR: profile hidden markov model based search for orthologs in ESTs.

Ebersberger I, Strauss S, von Haeseler A.

BMC Evol Biol. 2009 Jul 8;9:157.PMID: 19586527 [PubMed - indexed for MEDLINE]Related articlesFree article

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Pollock DD, Eisen JA, Doggett NA, Cummings MP.

Mol Biol Evol. 2000 Dec;17(12):1776-88. Review.PMID: 11110893 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogenetics of modern birds in the era of genomics.

Edwards SV, Bryan Jennings W, Shedlock AM.

Proc Biol Sci. 2005 May 22;272(1567):979-92. Review.PMID: 16024355 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 17962297 [PubMed - indexed for MEDLINE]Related articlesFree article

An approach of orthology detection from homologous sequences under minimum evolution.

Kim KM, Sung S, Caetano-Anollés G, Han JY, Kim H.

Nucleic Acids Res. 2008 Oct;36(17):e110. Epub 2008 Aug 1.PMID: 18676448 [PubMed - indexed for MEDLINE]Related articlesFree article

Investigating 42 candidate orthologous protein groups by molecular evolutionary analysis on genome scale.

Xie T, Ding D.

Gene. 2000 Dec 31;261(2):305-10.PMID: 11167018 [PubMed - indexed for MEDLINE]Related articles