Before running ACT you will need to obtain a comparison, which is usually the result of a blastn or tblastx search of a sequence of interest against another. The blast output will need to be processed with MSPcrunch. ACT can only read MSPcrunch output created with with the -d flag.
Here is an example input file file generated by MSPcrunch -d.
1399 97.00 940 2539 sequence1.dna 1 1596 AF140550.seq 1033 93.00 9041 10501 sequence1.dna 9420 10880 AF140550.seq 828 95.00 6823 7890 sequence1.dna 7211 8276 AF140550.seq 773 94.00 2837 3841 sequence1.dna 2338 3342 AF140550.seq
The columns have the following meanings (in order): score, percent identity, match start in the query sequence, match end in the query sequence, query sequence name, subject sequence start, subject sequence end, subject sequence name.