Dendroscope is a software for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool.
LCR-eXXXplorer is a web-service designed to assist biologists in displaying, searching and sharing Low Complexity Regions (LCRs) contained within protein sequences.
UCSF clusterMaker is a Cytoscape plugin that unifies different clustering techniques and displays into a single interface. Current clustering algorithms include hierarchical, k-medoid, AutoSOME, and k-means for clustering expression or genetic data; and MCL, transitivity clustering, affinity propagation, MCODE, community clustering (GLAY), SCPS, and AutoSOME for partitioning networks based on similarity or distance values. Hierarchical, k-medoid, AutoSOME, and k-means clusters may be displayed as hierarchical groups of nodes or as heat maps. All of the network partitioning cluster algorithms create collapsible “meta nodes” to allow interactive exploration of the putative family associations within the Cytoscape network, and results may also be shown as a separate network containing only the intra-cluster edges, or with inter-cluster edges added back
FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).
InterViewer is a software for visualizing large-scale protein interaction networks. InterViewer (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component, and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of InterViewer over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases, and (3) it provides several operations for effectively exploring large-scale protein interaction networks.
::DEVELOPER
Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon
GenomeStudio is a software to visualize and analyze data generated by all of Illumina’s platform.This powerful informatics solution supports the primary analysis of sequence-based data produced by the Genome AnalyzerIIx and microarray-based data generated by the iScan System. Performance optimized tools and a user-friendly graphical interface allow you to quickly and easily convert data into meaningful results for your genome analysis and research.
