TuneClustalX
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.
Alignments can often be improved by using different gap penaties for
a selected portion of the alignment. ClustalX allows you select a
range of residues and apply a set of gap penalties only to that range.
The effectiveness of that change can be determined by TuneClustalX by using
the option to report the average Q-score for only that selected range.
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