Download and install Sequencher 5.4.6 and install it. If it doesn't start automatically, launch it after it has been installed.
When it starts up you will be asked to set your license...
OK. I'm not really sure if that's going to happen. In my tests it doesn't ask but other documentation I've read claims that it will and I haven't been able to reliably test on a system that hasn't already had it installed. I have gone to some length to sanitize the test system but I can't be sure what's going to happen.
Anyways, when it starts up you may be shown a license dialog and asked to select one of several options which will include something like I have a license file...
. Select that one and when it opens the file selector dialog, navigate to where-ever you put the file downloaded in the previous step and select it.
It should read the file and hopefully continue starting up without any further fuss.
What actually happens to me when I try this is that I install the KeyAccess program and tell it to use retromac2... Then I install Sequencher and after the installation it starts up in full licensed mode and doesn't ask any questions about the license. Sounds easy, right? Don't worry, I'm sure it won't work that way for you. Let me know what happens when it bombs.