On Unix and GNU/Linux the easiest way to run the program is to run the script called act in the ACT installation directory (see the section called Getting and Installing ACT in Chapter 1) like this:
~/act/act
If all goes well you will be presented with a small window with one menu (the File menu). See the section called The ACT Launch Window for a description of this window.
Alternatively you start ACT with the names of two sequence/EMBL/GENBANK files and a file containing the comparison data eg:
~/act/act sequence1 blast_output.crunch sequence2
If you have more than two sequences (there is no upper limit) they should be listed on the command line separated by the corresponding comparison file:
~/act/act sequence1 seq2_v_seq1.crunch sequence2 seq3_v_seq2.crunch sequence3
See the section called UNIX Command Line Arguments for ACT for a list of the other possible command line arguments.
Here is an alternative way to run ACT if the act script doesn't work for you:
cd ~/act
java -Dartemis.environment=UNIX -classpath .:./lib/biojava.jar:./lib/jakarta-regexp-1.2.jar:./lib/jemAlign.jar -Dartemis.environment=UNIX uk.ac.sanger.artemis.components.ActMain