Many EMBOSS applications have common functionality. For instance, the majority read or write molecular sequences, which might have features associated with them, or which have been aligned by some other program. Support for sequences, features and alignments is consistent across the package; all applications support the same formats and are configurable in a similar manner. Where other types are data are handled, common file formats, called report formats, are used. This chapter describes the common features of the supported file formats and includes examples of all of the supported sequence, feature, alignment and report formats.