Biovisualization Links Page

LInks to software for and examples of biovisualization.

• Home Page for Processing - download code, tutorials .
• Repository of user-submitted Processing programs.
• JMOL Gallery.
• A tool for drawing phylogenetic trees
• Dendroscope - another tree drawing tool
• Tool for visualizing large networks/graphs in bioinformatics (and other domains)
• A nice graph drawing applet with lots of options
• Tutorial on Molecular Visualization
• Index of Molecular Visualization Resources
• VizBI: Visualizing Biological Data
• Many Eyes public data visualizations
• TextArc document visualizations

• Description of Common Nucleotide and Protein Sequence File Formats
• Description of Newick Format for Trees
• A Primer on GraphML, a Common Graph File Format
• A Converter for common molecular formats

• Gravitational forces on blobby objects
• Cells made with moving centers and Voronoi polygons
• Game of Life

• PubMed literature references
• International Society for Computational Biology
• National Center for Biotechnology Information
• European Bioinformatics Institute
• GenBank, DDBJ, EMBL nucleotide sequence databases
• Swiss-Prot Protein Database
• Protein Structure Database
• Human and mouse genome
• 1000 human genomes project
• Catalog of common genetic variants in humans
• Kyoto Encyclopedia of Genes and Genomes
• Collection of gene variation (mostly SNP) databases
• Blast homology search tool
• Database search tool

• Jalview alignment editor tool
• ClustalW multiple alignment tool
• Plink analysis tool
• Artemis: Genome Browser and Annotation Tool
• List of genetic analysis tools
• Bioconductor analysis tool
• RMAExpress - tool to compute gene expression summary values
• Cluster 3.0 - hierarchical clustering of gene experssion data
• Java Treeview - gene expression visualization tool
• Bioinformatics Tool List from UMASS Medical School

• Understanding Bioinformatics, by Zvelebil and Baum
• Bioinformatics: Sequence and Genome Analysis, by Mount