It's a shame that the two known web-based resource (webact and double act) created for generating comparison files are no longer working. You can find your way around it if you have a computer that works in a unix-like environment (MacBook or Linux Ubuntu).
In a terminal, typed the following command:
sudo apt-get install ncbi-blast+ (to downloaded Blast) makeblastdb -in Genome1 -dbtype nucl blastn -query Genome2 -db Genome1 -evalue 1 -task megablast -outfmt 6 > Genome1_Genome2.crunch
make sure you have assembled genomes that you want to compare in your working directory
This link might also help: https://katholtlab.files.wordpress.com/2017/07/comparativegenomicstutorialv2.pdf
I wrote a script to do this some time ago as all the webservers are defunct.
An Artemis Comparison Tool file is simply a tabular blast output file.
NB, contrary to the title and tags of this question, ACT doesn’t handle multiple sequence alignments. It will only do pairwise alignments, thought you can visualise multiple pairs (e.g. A vs B, B vs C, and each pair will need it’s own comparison file.