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Full List(162)

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blast output parser
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Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.Artemis is written in Java, and is available for UNIX, Macintosh ...

A gene prediction tool for eukaryotes
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BLAST+ NCBI 2.2.29
  • Public BLAST using ViroBLAST interface.
  • Private BLAST restricted to the GenOak project.
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BWA

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Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. The former works for query sequences shorter than 200bp and the latter for longer ...

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a flexible suite of utilities for comparing genomic features.
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BioMart is a query-oriented data management system developed jointly by the Ontario Institute for Cancer Research (OICR) and the European Bioinformatics Institute (EBI).The system can be used with any type of data and is particularly suited for providing ...

New compact graphical representations have been developed (1) a chromosome cascading zoom allows the user to enlarge a region of chromosome as deep as he needs, while keeping an overview of the whole chromosome map. (2) A new compact QTL track summarizing QTL data ...

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WU-BLAST2 gapped blast and tools.Warning: this software is deprecated and has been replaced by AB-BLAST, which is not available at URGI.
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 The BLASTER suite gathers C++ programs developed for transposable element search and their annotation in large eukaryotic genome sequence. But we think that the tools are generic enough to be used in other contexts. The suite is composed by three programs BLASTER, MATCHER and GROUPER. ...

Fast sequence search command line tool.BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 25 bases, and ...

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Blocksearch search for protein motifs or patterns
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An ultrafast, memory-efficient short read alignerIt aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB ...

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Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.Bowtie 2 ...

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BreakDancer-1.1, released under GPLv3, is a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It includes two complementary programs.BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing ...

CMap is a web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data.
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Compares and masks protein or nucleotide sequences.
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Maize cell wall catalog
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Predict presence of chloroplast transit peptides
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Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.Circos is ideal for creating publication-quality infographics and illustrations with a high data-to-ink ratio, richly layered ...

Colin Dewey's software: RSEM, Mercator, FSA, parametric, etc
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Sequence contig, consensus, chromatogram editor (ace format)
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Gene ontology interface
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Sequence comparison
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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many ...

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DEA is a Galaxy workflow for the Differential Expression Analysis of RNA-Seq data between two conditions. It uses a bioinformatics protocol based on raw read counts from a mapping of the reads to the reference genome.DEA is composed of a RNA-Seq mapper (Tophat, Tophat2 ...

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Differential gene expression analysis based on the negative binomial distribution
Bioconductor version: Release (3.2)Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.Author: Michael Love (HSPH Boston), Simon Anders, Wolfgang Huber ...

DSK

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DSK is a k-mer counting software, similar to Jellyfish. Jellyfish is very fast but limited to large-memory servers and k ≤ 32. In contrast, DSK supports large values of k, and runs with (almost-)arbitrarily low memory usage and reasonably low temporary disk usage. ...

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Amino acid translation program for full-length cDNA sequences with frameshift errors
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EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even ...

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EMMA is a statistical test for model organisms association mapping correcting for the confounding from population structure and genetic relatedness. EMMA takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which allows us to sustantially ...

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Efficient Mixed-Model Association eXpedited (EMMAX) is a statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only ...

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This tool is based on genscan, which uses a Hidden Markov Model (HMM) to do gene prediction in DNA sequences.
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Produce colinear segments from extant genomes handling rearrangements
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  Ephesis, for Environment and Phenotype Information System, is a GnpIS module dedicated to the integration of experimental trial on Genotype X Environment studies. It allows to store data from any plant species studied at the INRA, whether annual species like wheat or perennial species ...

Pairwise sequence comparison.It includes a good model for gap alignment, especially EST to genome mapping.
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Predicting multiple genes in genomic DNA sequences.
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FPC

FPC (fingerprinted contigs) is an interactive program for building contigs from fingerprinted clones, where the fingerprint for a clone is a set of restriction fragments. FPC has an algorithm to automatically cluster clones into contigs based on their probability of coincidence score. For each ...

A quality control tool for high throughput sequence data.
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Sequence comparison
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The fast lexical analyser generator
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Sensitive peptide detection on noisy matured sequences
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FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
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The Genome Analysis Toolkit (GATK) is a software package developed to analyse next-generation resequencing data.
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 The Generic Genome Browser (GBrowse) is a genome viewer and is GMOD's most popular component. It is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.We use the GBrowse flexible adaptor ...

 The Generic Genome Browser (GBrowse) is a genome viewer and is GMOD's most popular component. It is a combination of database and interactive web pages for manipulating and displaying annotations on genomes.We use the GBrowse flexible adaptor ...

GBrowse_syn, or the Generic Synteny Browser, is a GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. It can be used to view multiple sequence alignment data, synteny or ...

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GRIT is genome-guided a transcript assembly tool designed and implemented by Nathan Boley, in collaboration with the Bickel and Celniker groups.
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Analysis of genomic data, configured with Biomart dataset, MAPHiTS tools and S-MART tools.Galaxy is an open, web-based platform for data intensive biomedical research. The Galaxy team is a part of BX at Penn State, and the Biology and

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Locate genes within a DNA sequence. Genemark hmm eucaryote coding region prediction (with hmm methods)
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Coding sequence prediction package
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A program to predict genes in anonymous genomic sequences designed with a hierarchical structure.
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A package for the fully automated processing of fingerprinting data from ABI 3100/3700 Genetic Analyzer.
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The GRS was developped to produce various and user-friendly web interfaces on genome annotations. It uses structural and functional annotations stored in Chado database (GMOD schema).
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The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.
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The versatile open source genome analysis software
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GigaBayes is the working name for a short-read SNP and short-INDEL discovery program. This version is specifically optimized for the analysis of large numbers (many millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes.The software takes advantage ...

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A Genomic Mapping and Alignment Program for mRNA and EST Sequences
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URGI Transcriptome web interface page.The database is a repository for all transcriptome data such as microarray or macroarray data.
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 GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. ...

Gnuplot is a portable command-line driven graphing utility. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. Gnuplot supports many types of plots in either ...

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HTSeq: Analysing high-throughput sequencing data with PythonHTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays
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HMMER is an implementation of profile hidden Markov models (profile HMMs) for biological sequence analysis. Profile HMMs are statistical models of multiple sequence alignments. They capture position-specific information about how conserved each column of the alignment is, and which residues are likely.More information is ...

Biological data warehouseInterMine is an open source data warehouse built specifically for the integration and analysis of complex biological data. Developed by the Micklem lab at the University of Cambridge, InterMine enables the creation of biological databases accessed by sophisticated web query tools. ...

Databases of protein domains and functional sites have become vital resources for the prediction of protein functions. During the last decade, several signature- recognition methods have evolved to address different sequence analysis problems, resulting in rather different and, for the most part, independent databases. ...

Isochore computational prediction
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Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) but is available as a general purpose alignment editor and analysis ...

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Jellyfish mer counter
What is it?
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can ...

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JIRA is a project tracking tool for teams building great software.JIRA sits at the center of your development team, connecting the team and the work being done. Track bugs and defects, link issues to related source code, plan agile development, monitor activity, report on ...

KisSplice is a piece of software that enables the analysis of RNA-seq data with or without a reference genome. It is an exact local transcriptome assembler that allows one to identify SNPs, indels and alternative splicing events. It can deal with an arbitrary number ...

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LUMPY is a framework for the discovery of structural variants (SV) that naturally integrates multiple SV signals jointly across multiple samples.
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A graphical viewer for pairwise sequence alignments.
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LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
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MAPHiTS: Mapping Analysis Pipeline for High-Throughput Sequences. PresentationIn the framework of large SNP discovery projects, we developed a novel “Mapping Analysis Pipeline for High-Throughput Sequences” (MAPHiTS). The pipeline allows the detection of single nucleotide polymorphisms (SNPs) and small insertion/deletions (indels) by comparing high-throughput Illumina ...

The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for networks (also known as graphs) based on simulation of (stochastic) flow in graphs. MCL has been applied in a number of different domains, mostly in bioinformatics. ...

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QTL mapping in multicross design
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A system for quickly aligning entire genomes.
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A multiple alignment sequence tool for amino acid or nucleotide sequences using Fast Fourier Transform.
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Whitehead's Genetic mapping tool
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Mapsembler2 is a targeted assembly software. It takes as input a set of NGS raw reads (fasta or fastq, gzipped or not) and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence ...

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A multiple alignment program for large genomic sequences
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Discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences
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MetaGPipe is a wrapper of the QIIME framework and FungalITSExtractor tool. It was especially designed to analyze PCR amplicons of fungal ITS regions sequenced with 454 technology. It was then successfully used with Illumina MiSeq reads.MetaGPipe extracts ITS regions from ...

Plant metabolome for genetic resource analysis, mutant and transformant screening and quantitative trait loci determination
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MOSAIK is a reference-guided assembler comprising of four main modular programs:
  •  MosaikBuild
  •  MosaikAligner
  •  MosaikSort
  •  MosaikAssembler.
 MosaikBuild converts various sequence formats into Mosaik’s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences. MosaikSort resolves paired-end ...

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mothur project a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
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Detecting tandem repeats in DNA sequences
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Multiple sequence comparison by log-expectation of amino acid or nucleotide sequences
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A tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed.
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coding region prediction
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Coding region prediction
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Fast and Accurate Spliced Alignments of Sequence Reads
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The PASTEClassifier (Pseudo Agent System for Transposable Elements Classification) is a transposable element (TE) classifier searching for structural features and similarity to classify TEs (Hoede C. et al. 2014). It browses the whole spectrum of ...

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Whole genome alignment software
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Computer science resources
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Sequence converter: format phred file in fasta format
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sequence assembly for phred files
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Sequence chromatogram base caller (ABI or SCF format)
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PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology. Since the original publication (Guindon and Gascuel 2003), PhyML has been ...

Phylogeny suite:
  • dnadist : DNA sequences (unix command dnadist)
  • dnapars : DNA sequences (unix command dnapars)
  • drawgram : Tree, plotting, consensus (unix command drawgram)
  • drawtree :Tree, plotting, consensus (unix command ...

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PHYTOPROT consists in performing an "all-by-all" comparison of (putative) protein sequences with the BIOFACET software, building clusters of sequences (Mohseni-Zadeh et al., Recomb 2003) based on their similarity and finally displaying à la Prodom the domains shared by the sequences ...

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SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM is described in the SAMtools project page.Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM ...

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Genomic repeat analysis software
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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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Multiple alignment sequence
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Synteny is gene's order conservation between differents species.Developed by URGI team for J. Salse (INRA Clermont-Ferrand).Publications:
  •  Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes.
Pont, Caroline; Murat, Florent; Guizard, Sebastien; Flores, Raphael; Foucrier, ...

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PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to ...

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SNPs and indels detection pipeline.
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Prediction: distinguish between mitochondrial and plastid targeting sequences
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Sequence primer searching
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Sequence primer searching and designing PCR primers
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Prot4EST is a computer program that takes expressed sequence tags (ESTs) and translates them to produce putative peptides.
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Prediction of protein subcellular localization sites from their amino acid sequences for plant.
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Prediction of protein subcellular localization sites from their amino acid sequences, for yeast and animals
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PyroBayes is a base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequencesMore information is available on Marth Lab Web page.
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QIIME is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field.QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial ...

R

Free software environment for statistical computing and graphics
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A package for automated de novo identification of repeat families from genomic sequences
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 The REPET package (Flutre T. et al, 2011, Quesneville H. et al. 2005) integrates bioinformatics programs in order to tackle biological issues at the genomic scale. It is distributed under the CeCILL license and deposited to the ...

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Multi-format sequence reader, reverse complement
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Identification of regulators of reproductive development and agronomic performances by inter-species promoter sequences analysis.
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It screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all ...

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RepeatScout is a tool to discover repetitive substrings in DNA
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S-MART manages your RNA-Seq and ChIP-Seq data. It also produces many different plots to visualize your data.PresentationSeveral tools are now available for mapping high-throughput sequencing data from a genome, but few can extract biological knowledge from the mapped reads. We have ...

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Short Oligonucleotide Analysis Package
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a short read de novo assembly tool
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an accurate consensus sequence builder
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Genome-wide ab initio detection of splice junction sites from RNA-Seq
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SRS

SRS is a data integration platform. it is a biowisdom software SRS offers the ability to query, to view and to link private and public databases.With its standardized interface, SRS ensures an easy use of several tools like for ...

Sam

Sequence alignment and modeling system
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Wide range of tools for alignments in the SAM or BAM format.More information on SourceForge.
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It is a Web-based Libre Software hosting system. It includes issue tracking (bugs, tasks, support, news and documentation), project member management by roles and individual account maintenance.
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A graphical multiple sequence alignment editor
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SignalP 3.0 predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of ...

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Genomic/cDNA sequence comparison
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Go to Siregal, the GnpIS Genetic resource module SIReGal, the Plant Genetic Resources Information System of the National Institut for Agronomical Research (INRA), France relies on a ...

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Specific Primers & Amplicon Design Software FUNCTIONGENOPLANTETMSPADS tries to design a unique GST (Gene-Sequence Tag) and a specific primer set for its PCR amplification, on a genomic sequence, knowing the gene structure. DESCRIPTIONIn transcriptome approaches, probes corresponding to individual members of multigenic families often lack specificity ...

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Splice Site Prediction (Arabidopsis, Maize)
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Splice Site Prediction (Arabidopsis, Human)
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sequence analysis package (alfsplit,assemble4,gap4 ...)
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Smith Waterman sequence comparison
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Prediction of transmembrane helices in proteins.
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Locate and display tandem repeats in DNA sequences.
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Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.
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TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). For the sequences predicted ...

Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.Last version: 1.2.2
  • Source code: 
  • Binary: 
  • Changes:
    • Removed autotools. It never like me.
    • Added a "version" parameter in command ...

A fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.More information is available on TopHat Web ...

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Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.The pipeline accepts assemblies that were generated across a wide range of k values in order to address variable transcript expression levels. It first filters and merges the multi-k assemblies, generating a ...

Computational structural and functional analysis of plant genomic sequences (BAC/Contigs/Scaffolds/Pseudomolecules)TriAnnot web pages
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Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.The current trimming steps are:
  • ILLUMINACLIP: Cut adapter and other illumina-specific sequences from the read.

Probably the most widely tool to search for tRNA genes in genomic sequence.A Web server is available at Lowe lab.
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UCLUST is a high-performance clustering, alignment and search algorithm that is capable of handling millions of sequences.Applications include:
  • Generating non-redundant protein and nucleotide sequence databases.
  • OTU-picking by clustering 16S/18S rRNA sequences.
  • Clustering reads from meta-genomic and environmental sequencing studies.
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VNAT is an information system for the study of the natural variation of Arabidopsis thaliana. It gives you access to
  • passport data including climatological and geographical information of ecotype origin
  • collection (core-collection, RILs populations)
  • characterization data.
You may also directly order seeds to ...

VarScan is a platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequencyh. Given data ...

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Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.http://www.ebi.ac.uk/~zerbino/velvet/
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Vitis sequences and polymorphisms management tool.Interface: PHPDatabase: MySQL
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The WebAGCoL package is a set of four tools: WebFPC displays contigs in a view very similar to the FPC display. WebChrom shows contigs and genetic markers aligned to the chromosome. It also allows the user to view the distribution of markers based on ...

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Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the ...

Electronic PCR (e-PCR) is computational procedure that is used to identify sequence tagged sites( STSs), within DNA sequences.
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De novo transcriptome assembler for very short readsOases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. It was developed by Marcel Schulz (MPI ...



Update: 02 Dec 2011
Creation date: 31 May 2011
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