Command

To run the program, type

ed [OPTION]...

where the options are

• -T n where $n$ is a positive integer: the number of calls to a subroutine allowed. If not specified, $T$ takes a very large value (namely, INFINTY in the code). Refer to [2] for the meaning of $T$.
• -in fileName where fileName is the name of the input file.
• -delete or -insert indicates if the genomes should be forced to contains the same set of genes by deletions or insertions of genes that appear in one but not the other genome. If none of them is specified, the program works as if -insert were specified. Refer to [2] for more details.
• -simplBB or -fastED or -approx indicates the algorithms used. It is either Sankoff's branch-and-bound approach, our divide-and-conquer approach or the approximation version of our divide-and-conquer approach. If none of them is specified, the program works as if -fastED were specified.
• -ebd or -erd indicate the distance used, either breakpoint distance or reversal distance. If none of them is specified, the program works as if -ebd were specified.

For example, a valid command could be: ed -in Genomes1 -erd -fastED -delete