Molecular phylogenetic analysis is one of the most important analysis methods in biology. If used well, it can help us understand how organisms diversified and how genes evolved. The methods of molecular phylogenetic analysis are subject to debate, so we are familiar with the mathematical background. However, we are not so familiar with how the data sets for phylogenetic analysis are made up. In this Biology Seminar, the main alignment algorithms for making data sets were explained and discussed. Scoring is important in alignment algorithms, and there was a discussion on scoring for amino acid and nucleic acid mutations and scoring for gap penalties. The discussion on alignment distance was also heated. I hope the audience all enjoyed it. I would like to have another discussion on phylogenetic analysis and mathematical background next time. Thank you very much!