Tool and references | Description | URL | Web-based or standalone |
---|---|---|---|
ABrowse [231] | A customizable genome browser framework | Web-based | |
AnnoJ [232] | A web 2.0 application designed for visualizing deep sequencing data and other genome annotation data | Web-based | |
Argo | Java tool for visualizing and manually annotating whole genomes | Standalone | |
Artemis [104] | Browser and annotation tool that allows visualization of sequence features, data and the results of analyses within the context of the sequence, and also its six-frame translation | Standalone | |
CGView [233] | Static and interactive graphical maps of circular genomes using a circular layout | Standalone | |
Combo [234] | Dynamic browser to visualize alignments of whole genomes and their associated annotations | Standalone | |
Annotation, analysis and display of vertebrates and other eukaryotic species | Web-based | ||
Family Genome Browser [235] | Visualizing genomes with pedigree information | Web-based | |
Gaggle [236] | Genome browser within an analysis framework; good microarray support | Standalone | |
A combination of database and interactive web pages for manipulating and displaying annotations on genomes | Web-based | ||
GenoMap [239] | A circular genome data viewer | Standalone | |
Genome Projector [240] | Circular genome maps, traditional genome maps, plasmid maps, biochemical pathways maps and DNA walks. Google API | Web-based | |
GenomeView [241] | Designed to visualize and manipulate a multitude of genomics data | Standalone | |
GenPlay [242] | A multipurpose genome analyzer and browser | Standalone | |
IGB [243] | Optimized to achieve maximum flexibility and high quality genome visualization | Standalone | |
IGV [222] | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets | Standalone | |
JBrowse [244] | A fast, embeddable genome browser built completely with JavaScript and HTML5 | Web-based | |
JGI | Supports live annotation; primary portal for DOE Joint Genomics Institute genome projects | Web-based | |
NCBI Genome Workbench | An integrated application for viewing and analyzing sequence data | Standalone | |
NCBI Map Viewer [245] | Vertically oriented viewer; integrated with NCBI resources and tools | Web-based | |
Phytozome [246] | A comparative platform for green plant genomics | Web-based | |
Savant [247] | It was primarily developed for visualizing sequencing data, although it can be used to visualize almost any genome-based sequence, point, interval or continuous dataset | Standalone | |
Scribl [248] | An HTML5 Canvas-based graphics library for visualizing genomic data over the web | Web-based | |
The HuRef Browser [249] | A web resource for individual human genomics | Web-based | |
The personal genome browser [250] | Visualizing functions of genetic variants | Web-based | |
Integration of clinical data | Web-based | ||
UCSC Genome Browser [103] | Rapid linear visualization, examination and querying of the data at many levels | Web-based | |
UTGB [253] | Open-source software for developing personalized genome browsers that work in web browsers | Web-based | |
X:map [254] | Mappings between genomic features and Affymetrix microarrays | Web-based |