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limit size of alignment generated by clustalw? Or related aligners?

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.

alignment fasta phylogenomics comparative-genomics
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written by user user

I think the question I need to ask is why do you want to do this? What is the goal? What scientific question do you think it will answer?

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written by Torst Torst

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