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The multiple sequence alignment (MSA) is a common entity in comparative analysis of sequences representing molecules such as DNA, RNA, and proteins. An MSA lines up the sequence building blocks (letters representing nucleotides for DNA/RNA and amino acids for proteins) to form the basis for a hypothesis of how the molecules have evolved, and is computed using, for example, software like Clustal Omega (Sievers & Higgins, 2014), MAFFT (Katoh & Standley, 2013), MUSCLE (Edgar, 2004), MACSE (Ranwez, Harispe, Delsuc, & Douzery, 2011), and hmmalign (Eddy, 2015). MSAs have many applications, from advanced analyses such as inferring evolutionary trees (phylogenies) or identifying function in subsequences, to basic use like visual inspection of data. We have written a tool named alv to support quick and basic viewing of MSAs (Arvestad, 2018).

alv: a console-based viewer for molecular sequence alignments