GRAPE 2.0 provides an extensive pipeline for RNA-Seq analyses. It allows the creation of an automated and integrated workflow to manage, analyse and visualize RNA-Seq data.
gff2ps is a program developed at Fundació Institut Mar d’Investigacions Mèdiques (IMIM) in collaboration with CRG (Roderic Guigó group), to visualize annotations of genomic sequences. The program takes as input the annotated features on a genomic sequence in GFF format, and produces a visual output in PostScript. It can be used in a very simple way, because it assumes that the GFF file itself carries enough formatting information, but it also allows through a number of options and/or a configuration file, for a great degree of customization.
For more information about this software, please click here
gff2ps is a program for visualizing annotations of genomic sequences. The program takes the annotated features on a genomic sequence in GFF format as input, and produces a visual output in PostScript. While it can be used in a very simple way, it also allows for a great degree of customization through a number of options and/or customization files.
Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.
Geneid is an ab initio gene finding program used to predict genes along DNA sequences in a large set of organisms. The program can be run through a web server (http://genome.crg.es/software/geneid/geneid.html) or downloaded and executed by command line
An automatic protein design algorithm that can be used to rationally modify protein stability, change protein specificity and affinity and predict metal binding sites. It can also be used to design protein-DNA interactions
FoldX is a computer algorithm developed to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. The predictive power of the algorithm has been tested on a very large set of point mutants spanning most of the structural environments found in proteins, as well as on protein complexes and protein-DNA complexes of medical and biotechnological relevance. FoldX uses a full atomic description of the structure of the proteins. The different energy terms taken into account in FoldX have been weighted using empirical data obtained from protein engineering experiments.
FoldX is being developed by the group of Luis Serrano at the CRG in Barcelona, Spain, in collaboration with Joost Schymkowitz and Frederic Rousseau and their team at the SWITCH Laboratory of VIB in Brussels, Belgium.
ETE (Environment for Tree Exploration) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees.
Toni Gabaldón
ETE (Environment for Tree Exploration) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. Besides a broad set of tree handling options, ETE’s current version provides specific methods to analyze phylogenetic and clustering trees. It also supports large tree data structures, node annotation, independent editing and analysis of tree partitions, and the association of trees with external data such as multiple sequence alignments or numerical matrices. ETE first version was developed in collaboration with Dr. Joaquín Dopazo lab at Centro de Investigación Príncipe Felipe (CIPF).
