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".
Alignment with Muscle
Alignment with Kalign