muscle

The premium Open Source alternative to Geneious

🎯 Best for:Large-scale phylogenetic analysis
Visit WebsiteCompare with Geneious
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GPL-3.0License

What is muscle?

Replaces proprietary sequence alignment software with a high-accuracy, scalable command-line tool. It utilizes a log-expectation score and tree-based refinement to handle thousands of sequences.

Tech Stack
C++Biology & Biotechnology

Why muscle?

  • High accuracy
  • Scalable to 10k+ sequences
  • Fast execution

Limitations

  • CLI only
  • No native GUI
  • Memory intensive
3/2/2026
Last Update
30
Forks
12
Issues
GPL-3.0
License
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Competitor Cost
-$1,440
/ year (est. based on Geneious)
Self-Hosted
$0
/ year
Team Size10 Users
150+
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