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MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.
Pryszcz LP, Huerta-Cepas J, Gabaldón T. Pryszcz LP, et al. Nucleic Acids Res. 2011 Mar;39(5):e32. doi: 10.1093/nar/gkq953. Epub 2010 Dec 11. Nucleic Acids Res. 2011. PMID: 21149260 Free PMC article.
Next station in microarray data analysis: GEPAS.
Montaner D, Tárraga J, Huerta-Cepas J, Burguet J, Vaquerizas JM, Conde L, Minguez P, Vera J, Mukherjee S, Valls J, Pujana MA, Alloza E, Herrero J, Al-Shahrour F, Dopazo J. Montaner D, et al. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W486-91. doi: 10.1093/nar/gkl197. Nucleic Acids Res. 2006. PMID: 16845056 Free PMC article.
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
Schlüter A, Fourcade S, Domènech-Estévez E, Gabaldón T, Huerta-Cepas J, Berthommier G, Ripp R, Wanders RJ, Poch O, Pujol A. Schlüter A, et al. Nucleic Acids Res. 2007 Jan;35(Database issue):D815-22. doi: 10.1093/nar/gkl935. Epub 2006 Nov 28. Nucleic Acids Res. 2007. PMID: 17135190 Free PMC article.
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Tárraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H. Tárraga J, et al. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W38-42. doi: 10.1093/nar/gkm224. Epub 2007 Apr 22. Nucleic Acids Res. 2007. PMID: 17452346 Free PMC article.
The human phylome.
Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T. Huerta-Cepas J, et al. Genome Biol. 2007;8(6):R109. doi: 10.1186/gb-2007-8-6-r109. Genome Biol. 2007. PMID: 17567924 Free PMC article.
PhylomeDB: a database for genome-wide collections of gene phylogenies.
Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T. Huerta-Cepas J, et al. Nucleic Acids Res. 2008 Jan;36(Database issue):D491-6. doi: 10.1093/nar/gkm899. Epub 2007 Oct 25. Nucleic Acids Res. 2008. PMID: 17962297 Free PMC article.
GEPAS, a web-based tool for microarray data analysis and interpretation.
Tárraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcárate S, Goetz S, Escobar P, Garcia-Garcia F, Conesa A, Montaner D, Dopazo J. Tárraga J, et al. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W308-14. doi: 10.1093/nar/gkn303. Epub 2008 May 28. Nucleic Acids Res. 2008. PMID: 18508806 Free PMC article.
ETE: a python Environment for Tree Exploration.
Huerta-Cepas J, Dopazo J, Gabaldón T. Huerta-Cepas J, et al. BMC Bioinformatics. 2010 Jan 13;11:24. doi: 10.1186/1471-2105-11-24. BMC Bioinformatics. 2010. PMID: 20070885 Free PMC article.
The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes.
Huerta-Cepas J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldón T. Huerta-Cepas J, et al. Insect Mol Biol. 2010 Mar;19 Suppl 2:13-21. doi: 10.1111/j.1365-2583.2009.00947.x. Insect Mol Biol. 2010. PMID: 20482636
Assigning duplication events to relative temporal scales in genome-wide studies.
Huerta-Cepas J, Gabaldón T. Huerta-Cepas J, et al. Bioinformatics. 2011 Jan 1;27(1):38-45. doi: 10.1093/bioinformatics/btq609. Epub 2010 Nov 11. Bioinformatics. 2011. PMID: 21075746
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