The FASTA sequence file format is widely supported by bioinformatics tools. For a detailed description, see this Wikipedia entry about FASTA . Like most programs, MUSCLE does not support comment lines in FASTA data. The first character in a FASTA file must be a greater-than symbol ( > ), immediately followed by the label of the first sequence. Gaps in input sequences (dashes or dots, - and . ) are discarded. Gaps are inserted into alignments using dashes ( - ).
