The MetaFASTA format “extends” the popular FASTA sequence format to store meta-sequence information on a per-base (or per-amino acid) basis.
It can be also used as a multiple alignment format.
Heikki Lehväslaiho’s original specs for this format and the responses can be found here:
>test
ABCDEFHIJKLMNOPQRSTUVWXYZ
&charge
NBNAANCNJCNNNONNCNNUNNXNZ
&chemical
LBSAARCLJCLSMOIMCHHULRXRZ
&functional
HBPAAHCHJCHHPOHPCPPUHHXPZ
&hydrophobic
I & OIOIJOIIOOIOOOOUIIXOZ
&structural
ABAEEIEIJEIIEOAEEAAUIAXAZ'