Geneious is described as 'Combines all the major DNA and protein sequence analysis tools into one revolutionary software solution!' and is an app. There are more than 25 alternatives to Geneious for a variety of platforms, including Windows, Mac, Linux, Web-based and Self-Hosted apps. The best Geneious alternative is VectorBee, which is free. Other great apps like Geneious are AliView, Chromas, BioEdit and CLC bio.
Free platform for editing, analyzing, and visualizing DNA and protein sequences with tools for restriction digestion simulation, open reading frame detection, primer design, alignment, GC/CpG visualization, NCBI gene import, vector ordering, and project management.
AliView is yet another alignment viewer and editor, but this is probably one of the fastest and most intuitive to use, not so bloated and hopefully to your liking.
Two software applications are available from Technelysium: Chromas and ChromasPro.
BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP/7. An intuitive multiple document interface with convenient features makes alignment and manipulation of sequences relatively easy on your desktop computer.
Genophore is an application for searching and designing proteins. It also provides a suite of bioinformatics utilities and collaboration tools.
Software for viewing, editing and analyzing plasmid sequences.
Ridom TraceEdit is a cross-platform graphical DNA trace viewer and editor. TraceEdit displays the chromatogram files from Applied Biosystems automated sequencers and files in the Staden SCF format.
A full featured multiple sequence alignment editor, analyser and shading utility for Windows.
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Free, open source and actively developed.