Alignments of protein or nucleotide sequences are very important when it comes to analyzing sequences. They provide information about conserved sequence regions which can give hints to the function of the protein or its domains. Alignments are also very useful in predicting the structure of proteins, identifying new members of protein families, and infering the evolutionary history of the sequences. In this chapter we will use tools to generate alignments between two or more sequences.

Pairwise alignments are used to compare two sequences. Different variants exist, which compare sequences globally or locally.

Multiple sequence alignments are used for identifying and visualizing conserved regions in a family of homologous proteins. Phylogenetic methods depend on multiple alignments to infer the evolutionary history of the sequences.