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GENOMICS SOFTWARE


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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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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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Circos logo
Circos
Category: Genomics software

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. Although originally designed for visualizing genomic data, it can create figures from data in any field. It requires PERL software language.

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Integrative Genomics Viewer (IGV) logo
Integrative Genomics Viewer (IGV)
Category: Genomics software

The Integrated Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations.

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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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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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VAAST logo
VAAST
Category: Genomics software

VAAST (the Variant Annotation, Analysis and Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases.

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AltAnalyze logo
AltAnalyze
Category: DNA microarray software, Genomics software

AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms, AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement).

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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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GERP logo
GERP
Category: Genomics software

Genomic Evolutionary Rate Profiling (GERP) identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as "Rejected Substitutions".

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JBrowse logo
JBrowse
The JBrowse Genome Browser
Category: Gene expression, Genomics software

JBrowse is a fast and full-featured scalable genome browser built completely with JavaScript and HTML5. It can run on your desktop, or be embedded in your website (see Bues et al., Genome Biol 17, 66 (2016) doi:10.1186/s13059-016-0924-1).

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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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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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PhageFinder logo
PhageFinder
From SourceForge
Category: Genomics software

Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences

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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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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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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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PROVEAN logo
PROVEAN
Category: Genomics software

PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2.

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PHAST logo
PHAST
Category: Genomics software

PHAST is a freely available software package (Cornell University) for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel).Like algorithms that assess protein-coding genes, they evaluate variants on the basis of how often the sequence changes between species

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AnnoVar logo
AnnoVar
Category: Genomics software

ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others).ANNOVAR is written in Perl and can be run as a standalone application on diverse hardware systems where standard Perl modules are installed.

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