ClustalX is a powerful and popular multiple sequence alignment program. The quality of an alignment depends upon the correct choice of gap penalties. While the default gap penalties for aligning DNA sequences are adequate, those for protein sequences are not optimal, and a better set of initial protein gap penalties have been found. Because the quality of a phylogeny can be no better than the quality of the underlying sequence alignment it is important to optimize the alignment for each particular set of sequences. ClustalX displays a histogram window that assists in judging the quality of an alignment, but it is difficult to visually compare an alignment with a previous alignment that used a different set of gap penalties. ClustalX can write the values of the Q-scores (the numbers represented by the histogram) to a file by choosing "Save Column Scores to File" from the Quality menu. TuneClustalX reads that file and calculates an average Q-score, making it easy to know if a modification of gap penalties has improved the alignment.
