TOPD/FMTS: a new software to compare phylogenetic trees. - Pere Puigbò; Santiago Garcia-Vallvé; James O. McInerney (Bioinform., 2007)

OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. - Pere Puigbò; Eduard Guzmán; Antoni Romeu; Santiago Garcia-Vallvé (Nucleic Acids Res., 2007)

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). - Pere Puigbò; Ignacio G. Bravo 002; Santiago Garcia-Vallvé (BMC Bioinform., 2008)

HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection. - Pere Puigbò; Antoni Romeu; Santiago Garcia-Vallvé (Nucleic Acids Res., 2008)

Comparison of Phylogenetic Trees and Search for a Central Trend in the "Forest of Life". - Eugene V. Koonin; Pere Puigbò; Yuri I. Wolf (J. Comput. Biol., 2011)