title: AQUA: automated quality improvement for multiple sequence alignments.
abstract: 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.
  
  
  BACKGROUND
  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 http://www.bork.embl.de/Docu/AQUA.
authors.affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany. muller@embl.de
authors.forename: Jean
authors.initials: J
authors.lastname: Muller
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Creevey
authors.forename: Julie D
authors.initials: JD
authors.lastname: Thompson
authors.forename: Detlev
authors.initials: D
authors.lastname: Arendt
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins