I have been in a discussion on a Fiddle Forum about using tools such as Notation Composer to help with intonation.
I disagreed with them because I thought Notation Musian/Composer isn't the best for intonation because I've been using it for almost 2.5 years and I think my intonation should be better and I've been trying recently to wean myself off MIDI based tools and use real recordings more. It's a very powerful tool though and I plan to continue using it for many other things.
Then someone in this thread on Intonation suggested taping down a "Drone" Key on a Key Board (tonic note of that Key) and play along with that to improve your intonation.
It so happens 2 hours later my Fiddle teacher suggested EXACTLY the same thing !!
So in stead of using a KeyBoard I used my "Programable KeyBoard" called Notation Composer and applied the drone suggestion to a Waltz in Notation Composer and I think it's working, but it's too soon to tell. There is something about the constant drone as reference vs the actually melody notes.
I used an organ for the instrument. Piano doesn't have enough sustain (which is my typical favorite MIDI instrument) and violin sounds awful. But the organ sounds pretty good.
http://softronix.com/fiddle/Music/Notation/Pretty_Peggy_Waltz.not
And for folks that run on Macs or don't feel like downloading Notation Composer Trial you can get an idea from the MIDI I exported.
http://softronix.com/fiddle/Music/Notation/Pretty_Peggy_Waltz.mid
So perhaps these MIDI tools can be more help for intonation than I thought