= Multiple sequence alignment
{wiki}
A <multiple sequence alignment> places three or more sequences in corresponding columns, inserting gaps where needed. The arrangement represents a hypothesis about positional correspondence and can support <phylogenetics> or detection of conserved motifs. A column can be reliably aligned in one region and ambiguous in another. Adding sequences can clarify shared structure but also introduce difficult divergent regions, so the alignment itself requires evaluation before downstream inference. <Amino acid substitution matrices from protein blocks by Steven Henikoff and Jorja G. Henikoff>[1992, conserved protein blocks and aligned positions]{ref}
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