Clustal X Alternatives

    Clustal X is described as 'Multiple sequence alignment software'. There are seven alternatives to Clustal X for a variety of platforms, including Windows, Linux, Mac, Online / Web-based and Self-Hosted solutions. The best alternative is Clustal Omega, which is free. Other great apps like Clustal X are UGENE (Free, Open Source), GeneDoc (Free), Geneious (Paid) and BioEdit (Free).

    This page was last updated Jan 18, 2021

    1. Clustal Omega is a multiple sequence alignment program. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.
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      • FreeOpen Source
      • Mac
      • Windows
      • Linux
      UGENE is free open-source cross-platform bioinformatics software.
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      • FreeProprietary
      • Windows
      A full featured multiple sequence alignment editor, analyser and shading utility for Windows. • Data analysis and visualization • Score assisted manual alignment • Paginated printouts • Windows based • Highly configurable • Exported figures • Phylognetic tree support
    2. Geneious combines all the major DNA and protein sequence analysis tools into one revolutionary software solution!
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      • FreeProprietary
      • Windows
      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.


      The program is no longer maintained. Last version, 7.2.5, released in December 2013, can be still downloaded from the official website.

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      • Free PersonalProprietary
      • Online
      • Self-Hosted
      • Software as a Service (SaaS)
      Integrated biological databases and bioinformatics tools.
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    3. QIAGEN CLC Main Workbench is ideal for DNA, RNA, & protein sequence data analysis with a wide variety of features, no advanced computer skills required! The workbench is available for Windows, Mac OS X, and Linux platforms.
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