You just need to chomp the user input before testing it. When the user enters 'l' or 'g', he also hits "enter", which appends a '\n' character at the end (newline). $alignment_type will never be equal to 'g' or 'l' until you've removed that newline character with chomp.

Just remember that anytime you read from a filehandle you need to account for trailing newline characters¹. chomp does that for you.

1. Unless the record separator has been changed or you're performed some other similar trickery. (update)