¶ Visualization
¶ Chemical Structure Visualization
¶ Data Visualization
- Caleydo Tools that focuses on biological data visualization
Clustergrammar Analyzing high-dimensional data as interactive hierarchically clustered heatmaps- CompNet A GUI based tool for comparison of multiple biological interaction networks
- Heatmapper Online application for visualizing various types of data as heat maps
- Intervene Tool for intersection and visualization of multiple gene or genomic region sets
- Jalview Program for multiple sequence alignment editing
- PCAGO Analyzing your RNA-Seq read counts with principal component analysis (PCA)
- RAWGraphs Open source data visualization framework
- SeaView Software to visualize alignment, create alignment and infer phylogeny
- UpSet Visualization technique for the quantitative analysis of sets
¶ Gene Neighborhood Figures Tools
- GCTNG Visualize the genomic context of a gene or a group of genes and their orthologous relationships
- Gene Graphics Application that allows for visually representations of physical gene neighborhoods
- SyntTax Synteny web service to take full advantage of the large amount or archaeal and bacterial genomes
¶ Genome Browsers Within Integrated Platforms
- GenomeProjector Zoomable user interface for molecular biology
- NCBI Genome Data Viewer
- PATRIC Data and analysis tools to support biomedical research on bacterial infectious diseases
¶ Miscellaneous
- IBS Assisting experimentalists in drawing publication-quality diagrams of both protein and nucleotide sequences
- VIZBI Blog A conference series bringing together researchers developing and using computational visualisation
¶ Motifs
- GeneBee Motifs Web tool that allows the construction of pairwise motifs
- Seq2Logo Sequence logo generator
¶ Pathways, Mapping Data To Pathways, Metabolic Reconstruction
- FungiPath Orthologous proteins in fungal genomes database
- MetaNetX Automated Model Construction and Genome Annotation for Large-Scale Metabolic Networks
- SIGNOR Organizes and stores in a structured format signaling information in mammals
¶ Sequence Data Visualization
- Berkeley WebLogo Designed to make the generation of sequence logos as easy and painless as possible
- MView Reformats the results of a sequence database search or a multiple alignment
- Two Sample Logos Calculates and visualizes differences between two sets of aligned samples of amino acids or nucleotides
¶ Structure Visualization Platforms
- Aquaria Allows for the visualization of protein structure of various proteins from numerous species
- Chimera Interactive visualization and analysis of molecular structures and related data
- Cn3D Allows you to view 3-dimensional structures from NCBI's Entrez Structure database
- EzMol Web server wizard for the rapid visualisation and image production of protein and nucleic acid structures
- iCn3D Viewer for interactive viewing of three-dimensional macromolecular structures and chemicals
- Jmol Viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules
- JPred A Protein Secondary Structure Prediction Server
- MolScript Creating detailed molecular graphics images from molecular 3D coordinates
- RasMol Biomolecular graphics for all
- Phyre Web-based services for protein structure prediction
- PyMOL Provide a means for creating high quality figures
- RCSB-PDB Makes PDB data available at no charge to all data consumers
- SWISS-MODEL Web-based integrated service dedicated to protein structure homology modelling
- Swiss PdbViewer Provides a user friendly interface allowing to analyze several proteins
¶ Tools to Make Figures
- ETE-Toolkit A Python framework for the analysis and visualization of trees
- EvolView Easy-to-use online tool for displaying, managing and customizing phylogenetic trees
- GraPhlAn Tool that produces high-quality, compact visualizations of microbial genomes
- iTOL Online tool for the display, annotation and management of phylogenetic trees
- Phylo.io Visualising and comparing phylogenetic trees
- Phandango Interactive viewer for bacterial population genomics
¶ Venn Diagram Tools
- BEG-Venn An interactive tool for comparing lists with Venn's diagrams
- BioVenn Comparison and visualization of biological lists using area-proportional Venn diagrams
- MetNetDB Information on networks of metabolic and regulatory and interactions in Arabidopsis
- OrthoVenn2 Platform for comparison and annotation of orthologous gene clusters among multiple species
- Stefanjol Venny Online venn diagram generator
- Venny An interactive tool for comparing lists with Venn's diagrams