This research deals with computational methods for solving algorithmic problems that arise in computational biology. It is centered around the analysis of biochemical networks, the reconstruction of phylogenies, and the application of graph grammars and graph transformation in computational and systems biology.

- Member, Algorithms, Bioinformatics, Complexity and Formal Methods Research Group, Technical University of Catalonia.
- Member, Computational Biology and Bioinformatics Research Group, Research Institute of Health Science, University of the Balearic Islands.
- Collaborator, Centre for Genomic Regulation, Barcelona Biomedical Research Park.

- Associate Editor, BMC Bioinformatics.

- Taxonomic Assignment in Metagenomics is a tool for the optimal taxonomic assignment of ambiguous pyrosequencing reads. Do not get confused with TANGO.
- NetTest is a tool analyzing phylogenetic networks.
- Alignment of Phylogenetic Networks is a tool for computing distances, aligning, and displaying phylogenetic networks.
- Taxonomic Coloring of Phylogenetic Trees is a tool for coloring a phylogenetic tree according to a reference taxonomy.
- Phylogenetic Reconstruction from Non-Genomic Data is a tool for clustering a set of organisms based on the similarity of their metabolic pathways.
- Bio::Tree::Compatible is a Perl module for testing compatibility of phylogenetic trees with nested taxa. It belongs to the BioPerl collection of Perl modules for computational biology.
- Bio::Tree::Supertree is a Perl module for combining phylogenetic trees with nested taxa into a common supertree.
- Bio::Tree::Draw::Cladogram
is a Perl
module for displaying phylogenetic trees
in EPS format. It belongs to the BioPerl
collection
of Perl modules for computational biology. Sample
display of a tree. Sample
comparative display of two trees.

- Chemistry::Artificial is a Perl module for building artificial chemistries.
- Chemistry::Reaction is a Perl module for modeling chemical reactions by means of edge relabeling graph transformation rules. It belongs to the PerlMol collection of Perl modules for computational chemistry written by Ivan Tubert-Brohman.

This research deals with pattern recognition problems in which objects are represented by attributed graphs. It is centered around a series of related problems: exact and approximate graph and subgraph isomorphism, and maximal common subgraph and minimal common supergraph.

- The experimental comparison of algorithms for exact subgraph isomorphism and related problems is facilitated by a simple benchmark, consisting of all pairs of graphs generated using the example graph parameters from Appendix C of The Stanford GraphBase: A Platform for Combinatorial Computing, which are of very diverse nature and range from 10 to 16796 vertices, with up to 328960 edges. Since there are 113 undirected graphs and 59 directed graphs, this benchmark provides for a total of 8211 problem instances. The graphs can be downloaded from sgb-graphs.tar.gz (11972 Kb) for use with The Stanford GraphBase, and from leda-graphs.tar.gz (7508 Kb) for use with LEDA.
- There is a Pattern Matching Pointers page, as well as a CPM Archive.

This research deals with specification problems whose static structure is represented by graphs and whose dynamics is described by graph transformations. It is centered around the use of algebraic methods in the study of graph rewriting, graph grammars, and graph transformation.

- Cooperate Researcher of EC Research TMR Network GETGRATS (General Theory of Graph Transformation Systems).
- Scientific Correspondent of ESPRIT Basic Research Working Group APPLIGRAPH (Applications of Graph Transformation).
- Former Scientific Correspondent of ESPRIT Basic Research Working Group COMPUGRAPH II (Computing by Graph Transformation).
- Grammatica
is a library of Mathematica functions for algebraic graph
transformation, built on top of the Combinatorica
package written by Steven
Skiena. A brief tutorial on
*Combinatorica*, based on the on-line help under Mathematica 3.0, is also available here - There is a Graph grammar bibliography, which belongs to the Bibliographies on Theory/Foundations of Computer Science section of the Collection of Computer Science Bibliographies
- There is also a Graph Grammars discussion list.

Gabriel Valiente