AQUA: automated quality improvement for multiple sequence alignments


UNLABELLED Multiple sequence alignment (MSA) is a central tool in most modern biology studies. However, despite generations of valuable tools, human experts are still able to improve automatically generated MSAs. In an effort to automatically identify the most reliable MSA for a given protein family, we propose a very simple protocol, named AQUA for 'Automated quality improvement for multiple sequence alignments'. Our current implementation relies on two alignment programs (MUSCLE and MAFFT), one refinement program (RASCAL) and one assessment program (NORMD), but other programs could be incorporated at any of the three steps. AVAILABILITY AQUA is implemented in Tcl/Tk and runs in command line on all platforms. The source code is available under the GNU GPL license. Source code, README and Supplementary data are available at

DOI: 10.1093/bioinformatics/btp651

1 Figure or Table


Citations per Year

51 Citations

Semantic Scholar estimates that this publication has 51 citations based on the available data.

See our FAQ for additional information.

Cite this paper

@article{Muller2010AQUAAQ, title={AQUA: automated quality improvement for multiple sequence alignments}, author={Jean Muller and Christopher J. Creevey and Julie Dawn Thompson and Detlev Arendt and Peer Bork}, journal={Bioinformatics}, year={2010}, volume={26 2}, pages={263-5} }