Dragonfly is a Web application for visualizing and analyzing partial-order alignments of protein sequences. It provides an interactive interface that enables users to view an alignment at various levels of granularity, to superimpose known sequence features onto the alignment, and to analyze the alignment in the context of similarity-based or taxonomy-based phylogenetic tree. Dragonfly supports identification of function or taxonomy specific conserved domains or motifs, and the development of their computational models in the form of PSSM or HMM profiles.