The output comparison is a bit better

This update removes some redundant for loops

It fixes an issue when the user gives an absolute or relative path using the -i option
The output no longer outputs all of the beast/mrbayes garbage that was going to the screen since the user really shouldn't care about that as they are only interested in the end result
I also converted all tabs to 4 spaces, sorry about that it makes it harder to compare what I changed unless you do the split view