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EPSPSClass Author: Pere Puigbo, PhD Leino L, Tall T, Helander M, Saloniemi I, Saikkonen K, Ruuskanen S, Puigbo P. (2020) Classification of the glyphosate target enzyme (5-enolpyruvylshikimate-3-phosphate synthase) for assessing sensitivity of organisms to the herbicide. Journal of Hazardous Materials, S0304-3894(20):32546-2 The EPSPSClass web server classifies the Glyphosate's target enzymes (EPSPS) into sensitive (Class I) or resistant (class II, III and IV) to glyphosate. This classification is based on presence and absence of amino acid markers in the active site       GPT Author: Pere Puigbo, PhD Puigbo P, Major JM (2015) GPT: a web-server to map phylogenetic trees on a virtual globe. PeerJ PrePrints 3:e1040. GPT (Global Positioning Trees) is a web-server that maps phylogenetic trees on a virtual globe. This server has been designed to be an easy-to-use tool to track evolutionary processes and will be useful for phylogeographical and epidemiological studies. The GPT server minimally requires a phylogenetic tree and geographical coordinates of species to display the tree topology on Google Earth.       OPTIMIZER (Lite Version) Author: Pere Puigbo, PhD Puigbo P, Guzman E, Romeu A and Garcia-Vallve S (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.       CAIcal/E-CAI Author: Pere Puigbo, PhD Puigbo P., Bravo IG and Garcia-Vallve S. (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biology Direct, 3:38. 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. Puigbo P., Aragones L. and Garcia-Vallve S. (2010) RCDI/eRCDI: a web-server to estimate codon usage deoptimization. BMC Research Notes, 3:87. Truong P, Garcia-Vallve S, Puigbo P. (2020) An unsupervised algorithm for host identification in flaviviruses. Biorxiv (pre-print), https://doi.org/10.1101/2020.04.20.050047 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.       TOPD/fMtS Author: Pere Puigbo, PhD Puigbo P, Garcia-Vallve S and J.O. McInerney (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.       Highly Expressed Genes Database Author: Pere Puigbo, PhD      Simplified Version Puigbo P, Romeu A and Garcia-Vallve S. 2008. HEG-DB: a database of predicted highly expressed genes in prokaryotic complete genomes under translational selection.Nucleic Acids Research, 36:D524-D527. The HEG-DB is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index for all of the genes using the codon usage of the highly expressed genes as a reference set. The "Pathway Tools Omics Viewer" from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes.       Horizontal Gene Tranfer Database Author: Santiago Garcia-Vallve, PhD      Old version S. Garcia-Vallve, E. Guzman, MA. Montero and A. Romeu. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Research, 31:187-189. The HGT-DB is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. The current version of the database includes the analysis of 94 bacterial and archaeal complete genomes, including multiple chromosomes and strains, when available. Other complete genomes will be added progressively.       DendroUPGMA Author: Santi Garcia-Vallve, PhD Garcia-Vallve S, Palau J and Romeu A. (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. ORFsearch       ORFsearch Author: Pere Puigbo, PhD Puigbo P et al. (2006) ORFsearch at URL: http://genomes.urv.cat/ORFsearch A web server utility that search Open Reading Frames or translates DNA sequences. Translate       Translate Author: Santi Garcia-Vallve, PhD S. Garcia-Vallve 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. LDIST       Levenshtein distance Author: Pere Puigbo, PhD Minimum number of single-character edits (insertions, deletions or substitutions) to transform one word into the other.