I am giving clustalw a set of sequences in FASTA format, each of length 5 (5 bases per sequence) using pretty much the default settings. Clustalw uses gaps in the resulting alignment and so the size of the resulting alignments can be quite long, e.g. 10 bases depending on size of the input. How can I set a limit on the length of alignments generated by clustalw? Do I need to give it a stronger gap penalty? I don't see a parameter in the docs that control the length of alignments specifically.