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Updated: Jun 18, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

AQUA: automated quality improvement for multiple sequence alignments.

Jean Muller¹, Christopher J Creevey, Julie D Thompson

¹European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany. muller@embl.de

Bioinformatics (Oxford, England)

|November 21, 2009

Summary

This summary is machine-generated.

This study introduces AQUA, an Automated quality improvement for multiple sequence alignments protocol. AQUA aims to automatically identify the most reliable multiple sequence alignments for protein families, improving upon existing methods.

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Published on: February 5, 2014

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

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Published on: February 10, 2023

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

Multiple sequence alignment (MSA) is fundamental in modern biological studies.
Human experts can still enhance automatically generated MSAs, indicating room for improvement in automated methods.

Purpose of the Study:

To develop a protocol for automatically identifying the most reliable multiple sequence alignment (MSA) for a given protein family.
To improve the quality of automated MSAs through a systematic approach.

Main Methods:

The proposed protocol is named AQUA (Automated quality improvement for multiple sequence alignments).
The current AQUA implementation integrates MUSCLE and MAFFT for alignment, RASCAL for refinement, and NORMD for assessment.
The system is designed to be modular, allowing for the incorporation of alternative programs in the future.

Main Results:

AQUA provides a method to automatically assess and improve the reliability of MSAs.
The protocol aims to reduce the need for manual expert intervention in MSA generation.

Conclusions:

AQUA offers a simple, automated solution for enhancing the quality of multiple sequence alignments.
The protocol has the potential to streamline bioinformatics workflows by providing more reliable MSAs.
The AQUA protocol is implemented in Tcl/Tk, runs on the command line, and is available under the GNU GPL license.