Ghemical
Avogadro
BKchem
GPeriodic
pymol
Jmol
Gnome Chemistry Utils
ChemDoodle
DNADynamo
SnapGene Viewer
BioEdit
UGENE
Geneious
Benchling
Genophore
Chromas
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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!
Avogadro - Avogadro is a free, fantastically easy to use molecule editor.
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.
BKchem - BKChem is a free (as in free software :o) chemical drawing program.
BioEdit - Biological sequence alignment editor
GPeriodic - GPeriodic is a periodic table application for Linux.
UGENE - UGENE is free open-source cross-platform bioinformatics software
