The aligned FASTA format read and written by Multalign Viewer is a simple variant of standard FASTA format. To make an aligned FASTA file, individual sequences in FASTA format are concatenated together and made the same length by including characters for leading, trailing, and gap positions. For the purposes of Multalign Viewer, any non-alphanumeric characters are tolerated in these positions. In apoex.fa, for example, leading and trailing positions are indicated by tildes (~) and gap positions are indicated by periods (.).