I'm not that good in musical theory, feel free to correct.
- Only a Matter of Time has several. I think it's mainly in C# minor, but the keyboard break is in F minor and the outro in E major. I think some of it is in F# minor.
- A Fortune in Lies begins in B minor, verses are in F# minor, chorus in A minor. There's also a riff in E minor.
- Learning to Live. Intro on F# minor, first verse and the chorus in E minor. Instrumental section has both. Outro in E minor.
- Metropolis pt.1 keeps shifting between E minor and B minor.
- The Mirror is in B minor, except for the chorus, which is in E minor.
- Blind Faith shifts between D minor (verse) and A minor (chorus). Instrumental section mostly in A minor.
- The Great Debate is mostly in E major, the heavy section in D minor.
- In the Name of God mostly in C minor, chorus in F minor.
- Repentance, intro in C# minor, verses and beginning of the chorus in E minor, solo and the post-verse/solo/outro in F# minor.
- Pull Me Under mostly in E minor, chorus in A minor. So as you might guess, it also applies to On the Backs of Angels.
There are many more... they're progressive band after all... and you'll need someone sober and competent to figure them out
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