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Tools

Tools are in free access Public access or restricted access Registered access

They run on the web, unix or both.

Tools in restricted access can use unpublished data.


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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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Galaxy is no more maintained at URGI
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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 ...

Update: 02 Dec 2011
Creation date: 31 May 2011