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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