Rasmol
pymol
UCSF Chimera
Jmol
VMD - Visual Molecular Dynamics
Avogadro
QuteMol
RasTop
DNADynamo
SnapGene Viewer
BioEdit
UGENE
Geneious
Benchling
Chromas
Genophore
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There are several DNA analysis apps. But most of them are subscription-based. DNADynamo is a static license app. It means that once you purchase a license, you get full support for these licenses, including future updates. We have five licenses in my lab, and I can easily transfer the licence on the computer of the finished student to the one who has just started. The interface is improving with every update, and I can say I love the app!
pymol - PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating...
SnapGene Viewer - SnapGene offers the fastest and easiest way to plan, visualize, and document DNA cloning and PCR. You can easily annotate features and design primers.
UCSF Chimera - UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular...
BioEdit - Biological sequence alignment editor
Jmol - Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry...
UGENE - UGENE is free open-source cross-platform bioinformatics software