This defines a multiple alignment in vertical format. The print_vertical command produces a file in 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. '*'
Simple example:
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 by MULTALIGN 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 * *iteration 2 a a p avg llg lcr gpg www s *
Examples: See bash.bloc, bash_vg.bloc and globin.bloc.
The block_filemay also encode regions to apply variable gap_penaltieswithin. See bash_vg.bloc for example syntax.