From Bioinformatics.Org Wiki
- ATV - Phylogenetic tree visualization
- Friend - Friend, an Integrated Front-end Application for Bioinformatics
- Garlic - a free molecular visualization program
- GeneView II - Interactive GenBank Entry Visualization
- gff2ps - Converting genomic annotations in GFF format to PostScript
- ModView - ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.
- PyMol - PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations.
- rasmol - RasMol is a free program which displays molecular structure.
- VEGA - VEGA was developed to create a bridge between most of the molecular software packages, like BioDock, Quanta/CHARMm, Insight II, MoPac, etc. In this tool have been also implemented some features that are useful to analyze, display and manage the 3D struct
- VMD - VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting
- UGENE - UGENE is a program to visualize and analyze sequences, alignments, phylogenetic trees, 3D protein structures