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This is Fixed format file that defines the order of alignment.

Each line gives three numbers, A, B, C.

A is an index to which sequence in the seq_file should be aligned next,
B gives the alignment score that was obtained with...
C which is the sequence that gave the score with A.


MULTALIGN must have already read the seq_file before the order file is defined. the sequences are then re-ordered within the program to conform to the order specified by the order_file.

Examples: globin_pairs.ord

Source: output from program ORDER as a result of processing the results of a pairwise sequence comparison.