CIAlign: A highly customisable command line tool to clean, interpret and visualise multiple sequence alignments

This is the authors' abstract. We don't add key points for this paper.

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.