Phylogenomics and genome evolution through large-scale phylogenetics
n the genomic era it has been possible to move from the evolutionary analysis of single protein families (phylogenetics) to that of complete genomes and proteomes (phylogenomics). To achieve this transition new tools have been developed that allow the large-scale reconstruction of thousands of phylogenetic trees in an automatic way. This computerization of the whole process of tree construction often involves the use of standard parameters and conditions for all tree families, inevitably resulting in poor or incorrect phylogenies in many cases. Moreover, interpreting such type of complex data poses many difficulties and does require the development of novel algorithms, tools, forms of representing the data and even new semantics and concepts.
We combine the development of original algorithms to treat phylogenomic data with its application to gain knowledge on problems of biological relevance. In particular we are interested in developing post-processing methods to interpret sequence alignments and phylogenetic trees in a large-scale and to mine such data to find evidence for functional interactions between proteins.
PhylomeDB: a database for genome-wide collections of gene phylogenies.. Nucleic Acids Res.. 36:D491–D496.. 2008.