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I used Kalign and Muscle to align given sequences, the results are presented below. My question is, based on the two alignments which tool seems better? I would personally believe that the Muscle tool is better since it overall has fewer gaps than Kalign, however is fewer gaps favorable or gaps that are "continous"/almost present in all sequences favorable?

I know neither is very good but I am asked to chose one or the other as "best".

Thank you!

Alignment with Muscle

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Alignment with Kalign

enter image description here

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    $\begingroup$ The difference is driven by different alignment penalties. Your sequences start with ATG, which would suggest they are protein: an insertion of one base is not okay from an evolutionary perspective nor is a 5 base insertion. In fact your second sequence has really few common bases in both —is it really a homologue? $\endgroup$ Oct 8 at 17:59

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