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GENOMICS SOFTWARE


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Galaxy logo
Galaxy
Category: Genomics software

Galaxy is an open, web-based platform for data intensive biomedical research, now available as a "cloud computing" resource Whether on this free public server or your own instance, you can perform, reproduce, and share complete analyses.

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Eisen Lab Software logo
Eisen Lab Software
Genomics software tools
Category: Genomics software

We are not a software development lab, but we develop a lot of software tools to support our research and make it all available for anyone to use and repurpose.

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ArrayOligoSelector logo
ArrayOligoSelector
Category: Genomics software

ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.

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GenePattern logo
GenePattern
Category: Genomics software, Proteomics software

GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

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Argo Genome Browser logo
Argo Genome Browser
Category: Genomics software
Subcategories: Broad

The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes. It's a free and open source standalone Java 1.4 application.

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Infernal logo
Infernal
Category: Genomics software

Infernal (inference of RNA alignments) is a software package for searching DNA sequence databases for RNA structure and sequence similarities. It allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments.

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Sybil logo
Sybil
From SouceForge
Category: Genomics software

Sybil is a web-based software package for comparative genomics. It was developed by the Bioinformatics department at The Institute for Genomic Research (TIGR) and development continues at the J. Craig Venter Institute and Institute for Genome Sciences (IGS) at the University of Maryland Baltimore's School of Medicine. The project has been funded by a variety of sources including: The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Center

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PhageFinder logo
PhageFinder
From SourceForge
Category: Genomics software

Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences

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MUMmer logo
MUMmer
From SourceForge
Category: Genomics software

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included wit

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DAGchainer logo
DAGchainer
Category: Genomics software

The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regi

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Glimmer logo
Glimmer
Category: Genomics software

Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.

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SMS Sequence Manipulation Suite logo
SMS Sequence Manipulation Suite
Category: Genomics software

The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

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JaMBW 1.1 logo
JaMBW 1.1
Category: Genomics software

JaMBW, the Java based Molecular Biologist's Workbench, is an online platform that had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use.

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JDotter logo
JDotter
Category: DNA alignment, Genomics software

Java Dot Plot Alignments (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly s

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