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Toolkit for cleaning and interpreting multiple sequence alignments

Project description



CIAlign documentation is now available via ReadTheDocs



  • python >= 3.6
  • matplotlib >= 2.1.1
  • numpy >= 1.16.3
  • scipy >= 1.3.0

The easiest way to install CIAlign is using conda or pip3.


conda install -c bioconda cialign


pip3 pip3 install cialign


Download The current release of CIAlign can also be downloaded directly using this link,

If you download the package directly, you will also need to add the CIAlign directory to your PATH environment variable as described here


CIAlign allows the user to:


  • Remove sources of noise from an MSA
    • Remove sequences above a threshold level percentage of divergence from the majority.
    • Remove insertions which are not present in the majority of sequences.
    • Crop poorly aligned sequence ends.
    • Remove short sequences below a threshold number of bases or amino acids.
    • Remove columns containing only gaps.
    • Remove either end of an alignment where columns don't meet a minimum identity threshold and coverage level.


  • Visualise alignments.
    • Generate image files summarising the alignment.
    • Label these images to show how CIAlign has affected the alignment.
    • Draw sequence logos
    • Plot alignment statistics - visualise coverage and conservation at each position in the alignment.


  • Generate consensus sequences.
  • Generate position frequency, position probability and position weight matrices
  • Format these matrices to be used as input for the BLAMM and MEME motif analysis tools.
  • Generate a similarity matrix showing the percentage identity between each sequence pair.


  • Extract a section of the alignment.
  • Unalign the alignment.
  • Replace U with T, or T with U in a nucleotide alignment.

CIAlign is designed to be highly customisable, allowing users to specify exactly which functions to run and which settings to use.

It is also transparent, generating a clear log file and alignment markup showing exactly how the alignment has changed and what has been removed by which function.


If you found CIAlign useful, please cite:

Tumescheit C, Firth AE, Brown K. 2022. CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments. PeerJ 10:e12983

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