Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species. - Hernán Dopazo; Javier Santoyo; Joaquín Dopazo (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Infering Non-Neutral Evolution within the Context of a Growing Genomic Framework: Preliminary Results using Human-Chimp Proteomes. - Leonardo Arbiza; Joaquín Dopazo; Hernán Dopazo (Spanish Bioinformatics Conference, 2004)

PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. - Lucía Conde; Juan M. Vaquerizas; Hernán Dopazo; Leonardo Arbiza; Joke Reumers; Frederic Rousseau 001; Joost Schymkowitz; Joaquín Dopazo (Nucleic Acids Res., 2006)

Positive Selection, Relaxation, and Acceleration in the Evolution of the Human and Chimp Genome. - Leonardo Arbiza; Joaquín Dopazo; Hernán Dopazo (PLoS Comput. Biol., 2006)

From genes to functional classes in the study of biological systems. - Fátima Al-Shahrour; Leonardo Arbiza; Hernán Dopazo; Jaime Huerta-Cepas; Pablo Minguez; David Montaner; Joaquín Dopazo (BMC Bioinform., 2007)

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. - Joaquín Tárraga; Ignacio Medina; Leonardo Arbiza; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (Nucleic Acids Res., 2007)

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. - Rubén Sánchez 002; François Serra; Joaquín Tárraga; Ignacio Medina; José Carbonell; Luis Pulido; Alejandro de María; Salvador Capella-Gutiérrez; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (Nucleic Acids Res., 2011)

Natural Selection on Functional Modules, a Genome-Wide Analysis. - François Serra; Leonardo Arbiza; Joaquín Dopazo; Hernán Dopazo (PLoS Comput. Biol., 2011)