Software

Software

Type:
Application/Software

GenNon-h is a software designed to generate multiple sequence alignments of DNA evolving on any phylogenetic tree.

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gff2aplot is a program to visualize the alignment of two sequences together with their annotations.

Type:
Application/Software

 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.

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gff2ps is a program for visualizing annotations of genomic sequences.

Type:
Application/Software

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.

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gff2ps is a program for visualizing annotations of genomic sequences

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

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This site provides a series of programs for the functional investigation of groups of genes, based on the Gene Ontology resource.

Category:
Gene Analysis

This site provides a series of programs for the functional investigation of groups of genes, based on the Gene Ontology resource.

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GRAPE 2.0 provides an extensive pipeline for RNA-Seq analyses.

Type:
Application/Software

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.

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HiC-inspector, a bioinformatics pipeline to facilitate the analysis of HiC dataset.

Type:
Application/Software
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The integrative pipeline for splicing analyses

Type:
Application/Software

The integrative pipeline for splicing analyses (IPSA); 1) Quantifies splice junctions and splice boundaries; 2) Calculates splicing indices, exon- and intron-centric; 3) analyzes micro-exons and local splice-graph structure

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Type:
Application/Software

IRBIS is a computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences

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meta is a program to produce and to align the TF-maps of two gene promoter regions.

Type:
Application/Software, Webservice

meta is a program is a program developed at Fundació Institut Mar d’Investigacions Mèdiques (IMIM) in collaboration with CRG (Roderic Guigó group) to produce and to align the TF-maps of two gene promoter regions. meta is very useful to characterize promoter regions from orthologous genes, or from co-regulated genes in microarrays, as it reduces the signal/noise ratio in a very significant manner, still detecting the real functional sites.

For more information about this software, please click here

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MetaPhOrs is a public repository of phylogeny-based orthology and paralogy predictions for most species with fully-sequenced genomes.

Category:
Gene Analysis

MetaPhOrs is a public repository of phylogeny-based orthology and paralogy predictions for most species with fully-sequenced genomes.

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mmeta is a program to produce and to align the TF-maps of multiple promoter regions.

Category:
Gene Analysis
Type:
Application/Software, Webservice

mmeta is a program to produce and to align the TF-maps of multiple promoter regions. mmeta is very powerful to characterize promoter regions from multiple orthologous genes, or from co-regulated genes in microarrays, as it reduces the signal/noise ratio in a very significant manner, still detecting the real functional sites.

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MyMpn is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections.

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Type:
Application/Software

Nextflow is a pipeline orchestration tool that provides a domain specific language (DSL), meant to simplify the writing of complex distributed computational workflows in a portable and replicable manner. It allows the seamless parallelization and deployment of any existing application with minimal development and maintenance overhead, irrespective of the original programming language.

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overlap is a program that computes the overlap between two sets of genomic features.

Category:
Gene Analysis
Type:
Application/Software

overlap is a program that computes the overlap between two sets of genomic features. More precisely it takes two gff files of genomic features as input and for each feature of the first set, says whether it is overlapped by a feature of the second set (basic mode, however more and more precise information can be retrieved).

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