UGENE Alternatives

UGENE is described as 'Is free open-source cross-platform bioinformatics software' and is an app in the education & reference category. There are more than 25 alternatives to UGENE for a variety of platforms, including Windows, Linux, Mac, Web-based and Self-Hosted apps. The best UGENE alternative is VectorBee, which is free. Other great apps like UGENE are AliView, BioEdit, Chromas and Genophore.

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UGENE alternatives page was last updated Feb 26, 2026

VectorBee
3 likes
VectorBee is a highly user-friendly genetic engineering software created by VectorBuilder for viewing, editing and analyzing DNA and protein sequences.
12 VectorBee alternatives
Cost / License
Free
Proprietary
Application type
DNA Editor
Origin
United States
Platforms
Windows
Mac
Linux
Is VectorBee a good alternative to UGENE?
AliView
3 likes
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.
Cost / License
Free
Open Source
Origin
Sweden
EU
Platforms
Mac
Windows
Linux
+1
Is AliView a good alternative to UGENE?
BioEdit
2 likes
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.
29 BioEdit alternatives
Cost / License
Free
Proprietary
Application type
DNA Editor
Alerts
Discontinued
Platforms
Windows
+2
Is BioEdit a good alternative to UGENE?
Chromas
1 like
Two software applications are available from Technelysium: Chromas and ChromasPro.
28 Chromas alternatives
Cost / License
Freemium
Proprietary
Application type
DNA Editor
Origin
Australia
Platforms
Windows
Is Chromas a good alternative to UGENE?
Genophore
2 likes
Genophore is an application for searching and designing proteins. It also provides a suite of bioinformatics utilities and collaboration tools.
29 Genophore alternatives
Cost / License
Free Personal
Proprietary
Platforms
Online
Self-Hosted
Software as a Service (SaaS)
Is Genophore a good alternative to UGENE?
Rasmol
2 likes
RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those found in the Protein Data Bank.
Cost / License
Free
Open Source
Platforms
Mac
Windows
Linux
Is Rasmol a good alternative to UGENE?
Geneious
1 like
Geneious combines all the major DNA and protein sequence analysis tools into one revolutionary software solution!
29 Geneious alternatives
Cost / License
Paid
Proprietary
Platforms
Mac
Windows
Linux
+1
Is Geneious a good alternative to UGENE?
TreeView
1 like
Tree drawing software for Apple Macintosh and Windows.
Cost / License
Free
Proprietary
Platforms
Mac
Windows
Linux
Is TreeView a good alternative to UGENE?
Ridom TraceEdi
1 like
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.
Cost / License
Free
Proprietary
Platforms
Windows
Linux
Is Ridom TraceEdi a good alternative to UGENE?
GeneDoc
1 like
A full featured multiple sequence alignment editor, analyser and shading utility for Windows.
6 GeneDoc alternatives
Cost / License
Free
Proprietary
Platforms
Windows
Is GeneDoc a good alternative to UGENE?
A
A
Archaeopteryx
1 like
Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees.
Cost / License
Free
Open Source (LGPL-2.1)
Platforms
Mac
Windows
Linux
Java
A
Is Archaeopteryx a good alternative to UGENE?
Clustal X
1 like
Multiple sequence alignment software.
8 Clustal X alternatives
Cost / License
Free
Proprietary
Platforms
Mac
Windows
Linux
Is Clustal X a good alternative to UGENE?