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Department of Pathology


Researchers at Pathology have devised a highly customisable command-line tool to clean, interpret and visualise multiple sequence alignments


CIAlign effectively removes problematic regions and sequences from MSAs and provides novel visualisation options.


This tool can be used to fine-tune alignments for further analysis and processing.

The tool is aimed at anyone who wishes to automatically clean up parts of an MSA and those requiring a new, accessible way of visualising large MSAs.

CIAlign can be used to remove poorly aligned sequence ends, highly divergent sequences, non-majority insertions, short sequences and gaps from a multiple sequence alignment. 

It also allows the user to plot “mini alignments” - a novel visualisation method to give an overview of a large MSA in a manageable image size. 

Created by researchers Dr Katy Brown and Dr Charlotte Tumescheit of the Firth Lab - CIAlign is available at - why not give it a try and let them know what you think. 


Find out more about CIAlign on the PeerJ: