P. Puigbò, E. Guzman, A. Romeu and S. Garcia-Vallvé (2007) OPTIMIZER: A web server for optimizing the codon usage of DNA sequences. Nucleic Acids Research 35:W126-W131.

OPTIMIZER is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level. Users can introduce their own preference tables to be used in the optimization process or use pre-computed tables from several prokaryotic species under a strong translational selection. Three methods of optimization are available: the 'one amino acid - one codon' approach, a random approach or an intermediate one. Several options, such as avoiding specific restriction sites and several outputs, are also available. This server can be useful for predicting and optimizing the level expression of a gene in heterologous gene expression.

Puigbo P, Bravo IG and Garcia-Vallve S. 2008 E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics, 9:65.

This server performs several computations in relation to codon usage and the codon adaptation of DNA or RNA sequences to host organisms. The E-CAI server is a web-application and an executable program that calculates the expected value of the Codon Adaptation Index (CAI) for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected CAI therefore provides a direct threshold value for discerning whether the differences in the CAI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences.

P. Puigbò, S. Garcia-Vallvé and J.O. McInernet (2007) TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics, 23:1556-1558. doi: 10.1093/bioinformatics/btm135.

TOPD/FMTS is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees. The software implements several previously described methods and new algorithms for comparing phylogenetic trees. It combines the TOPD program (TOPological Distance), which compares two trees with the same taxa or two pruned trees, and the FMTS program (From Multiple To Single), which converts multi-gene family trees to single-gene trees.

S. Garcia-Vallve, J. Palau and A. Romeu (1999) Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Molecular Biology and Evolution 9:1125-1134.

Use this program to create a dendrogram from a set of variables. The program calculates a similarity coefficient between pairs of sets of variables, transforms these coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.

P. Puigbò et al. (2006) ORFsearch at URL: http://genomes.urv.es/ORFsearch

A web server utility that search Open Reading Frames or translates DNA sequences.

S. Garcia-Vallvé et al. (2002) Translate at URL: http://www.tinet.org/~debb/Translate/

Use this program to translate a set of DNA sequences and obtain the proteins encoded, the %G+C, the Codon usage, the amino acid composition or the RSCU values.