cialign 1.1.0

Toolkit for cleaning and interpreting multiple sequence alignments

CIAlign

CIAlign documentation is now available via ReadTheDocs

Summary

CIAlign allows the user to:

Clean

• 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

• 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.

Interpret

• 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.

Edit

• 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.

Citation

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 https://doi.org/10.7717/peerj.12983

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