Multalign Viewer displays sequence alignments and single sequences.
Sequence alignments can be read/written in aligned FASTA format, a simple variant of standard FASTA format. In an aligned FASTA file, all of the sequences are made the same length by including characters for leading, trailing, and gap positions. Multalign Viewer tolerates any non-alphanumeric characters in these positions. In apoex.fa, for example, leading and trailing positions are indicated by tildes (~) and gap positions are indicated by periods (.).
Single sequences can be read/written in standard FASTA format, but a file that contains multiple unaligned sequences (sequences of different lengths) will not be accepted.