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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.
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.
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H. Sánchez R, et al. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W470-4. doi: 10.1093/nar/gkr408. Epub 2011 Jun 6. Nucleic Acids Res. 2011. PMID: 21646336 Free PMC article.
Measuring guide-tree dependency of inferred gaps in progressive aligners.
Capella-Gutiérrez S, Gabaldón T. Capella-Gutiérrez S, et al. Bioinformatics. 2013 Apr 15;29(8):1011-7. doi: 10.1093/bioinformatics/btt095. Epub 2013 Feb 23. Bioinformatics. 2013. PMID: 23435067 Free PMC article.
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.
Huerta-Cepas J, Capella-Gutiérrez S, Pryszcz LP, Marcet-Houben M, Gabaldón T. Huerta-Cepas J, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D897-902. doi: 10.1093/nar/gkt1177. Epub 2013 Nov 25. Nucleic Acids Res. 2014. PMID: 24275491 Free PMC article.
A phylogenomics approach for selecting robust sets of phylogenetic markers.
Capella-Gutierrez S, Kauff F, Gabaldón T. Capella-Gutierrez S, et al. Nucleic Acids Res. 2014 Apr;42(7):e54. doi: 10.1093/nar/gku071. Epub 2014 Jan 29. Nucleic Acids Res. 2014. PMID: 24476915 Free PMC article.
Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. Altenhoff AM, et al. Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4. Nat Methods. 2016. PMID: 27043882 Free PMC article.
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes.
Cañada A, Capella-Gutierrez S, Rabal O, Oyarzabal J, Valencia A, Krallinger M. Cañada A, et al. Among authors: capella gutierrez s. Nucleic Acids Res. 2017 Jul 3;45(W1):W484-W489. doi: 10.1093/nar/gkx462. Nucleic Acids Res. 2017. PMID: 28531339 Free PMC article.
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, da Silva AS, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT; Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S; Quest for Orthologs Consortium. Forslund K, et al. Among authors: capella gutierrez s. Bioinformatics. 2018 Jan 15;34(2):323-329. doi: 10.1093/bioinformatics/btx542. Bioinformatics. 2018. PMID: 28968857 Free PMC article.
Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi.
Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T. Capella-Gutiérrez S, et al. BMC Biol. 2012 May 31;10:47. doi: 10.1186/1741-7007-10-47. BMC Biol. 2012. PMID: 22651672 Free PMC article.
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