MUSCLE manual
FASTA files
The FASTA sequence file format is widely supported by bioinformatics tools. For a detailed description, see this Wikipedia entry about FASTA.

MUSCLE allows lines of any length in a FASTA file. (Some programs limit lines to e.g. 80 characters).

MUSCLE does not support comments in FASTA files.

White space characters (blanks and tabs) are discarded if found in sequence data, but many other tools do not allow this and the practice is not recommended.