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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. Capella-Gutiérrez S, et al. Bioinformatics. 2009 Aug 1;25(15):1972-3. doi: 10.1093/bioinformatics/btp348. Epub 2009 Jun 8. Bioinformatics. 2009. PMID: 19505945 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.
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.
Comparative genomics-based prediction of protein function.
Gabaldón T. Gabaldón T. Methods Mol Biol. 2008;439:387-401. doi: 10.1007/978-1-59745-188-8_26. Methods Mol Biol. 2008. PMID: 18370117
Large-scale assignment of orthology: back to phylogenetics?
Gabaldón T. Gabaldón T. Genome Biol. 2008 Oct 30;9(10):235. doi: 10.1186/gb-2008-9-10-235. Genome Biol. 2008. PMID: 18983710 Free PMC article. Review.
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome.
Schlüter A, Real-Chicharro A, Gabaldón T, Sánchez-Jiménez F, Pujol A. Schlüter A, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D800-5. doi: 10.1093/nar/gkp935. Epub 2009 Nov 5. Nucleic Acids Res. 2010. PMID: 19892824 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.
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
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.
Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldón T. Huerta-Cepas J, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D556-60. doi: 10.1093/nar/gkq1109. Epub 2010 Nov 12. Nucleic Acids Res. 2011. PMID: 21075798 Free PMC article.
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