There are a lot of them. FASTA comes to mind. GenBank is another. Clustal, EMBL, GCG and the list goes on. I’d say FASTA is one of the most commonly used or accepted, but I could be wrong. Still, many databases and software programs have their own format that they accept and generate. Some of these programs and databases will accept several formats or generate files in several formats. It can get a bit confusing. So, you’ve got a sequence file in PAUP but you need it in FASTA? Don’t even know what format it is? Or what they look like or the information that they contain?
Here are some links that could help I have gathered over time and lately as I was working with a phylip file:
Oxford’s CGRB’s examples of sequence formats.
Here are two programs that will convert one format to another:
Hopefully that will get you started in making sense of sequence formats. Have another other help pages or conversion programs to suggest?