This should be in AMPS block file format.
The minimum requirements for a block file for N aligned sequences are 1. N '>comment line(s)' 2. '* iteration int' 3. 'N or more vertically aligned sequences' 4. '*'
The format allows several alternative alignments to follow each other providing they are identified by a different iteration number (eg. 1,2,3). Currently, SCANPS only reads the first alignment. See the AMPS documentation for further details of alternative multiple alignments.
This is a block file containing two alternative alignments of three sequences. The comments that I an writing here may appear in the block file, but are ignored when the file is read. The only proviso is that no 'greater than' or 'star' characters must be present. >first this is sequence A >second this is sequence B >third This is sequence C * iteration 1 A A P AVG LLG LCR G PG WWW S *