多重串行比对（Multiple sequence alignment；MSA）是对三个以上的生物学串行（biological sequence），如蛋白质串行、DNA串行或RNA串行所作的串行比对。一般来说，是输入一组假定拥有演化关系的串行。从MSA的结果可推导出串行的同源性，而种系发生关系也可引导出这些串行共同的演化始祖。如右图般的可视化叙述可描绘出各种突变事件，例如点突变的单格变化，或是如删除突变与插入突变，可使各个串行之间产生鸿沟。MSA常用来研究串行的保守性（conservation），或是蛋白质结构域的三级结构与二级结构，甚至是个别的氨基酸或核苷酸。

A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides.