Treat them as scales of their own. Say you are to solo over an A major chord. Now, instead of playing A Ionian over that A chord, play A Mixolydian, and that'd give you a bluesy sound. The reason you can play A Mixolydian over that A chord is that Mixolydian still has all the notes of the A chord, but it's different from the Ionian in that it has a minor 7th.
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a fun way think of modes is that theyre Church Scales..

no different than a scale really... just the name.

i dont get it either.
I learned a lot about this from Desi Serna's "Fretboard Theory" book. Breaks almost everything down that you ever wanted to know into easy bits. I've been playing over 30 yrs. and never 'got it' til I studied this - http://Guitar-Music-Theory.com It's got very easy ways to LEARN which modes to play over what, and how to REMEMBER which to play over which!
This lesson should help you. Also, read the MT FAQ, and, if you still don't understand, PM sinan90 or Johnljones.
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There's really 2 different ways to think about things when you're improvising:

1) Key Center
2) Modes

For most rock stuff, you really only need to be concerned with Key Center: what
key am I in? -- For overall resolution. And, secondarily, what the chords are doing
for emphasizing chord tones.

Modes are where you consider what the chord is and what the scale is in relation
to the chord.

Its much easier and more general to think in key center. Thinking modally, implies
you need to think about the mode on every single chord change. This knowledge
is useful everywhere, but more so in Jazz which can go through a lot of implied
and explicit key changes and where you do a lot more scale substitution.


Dm7 - G7 - Cmaj7. A II - V -I progression.

Key Center: it's all in C so I'll use C major. I need to be aware of resolving to chord
tones over Cmaj 7.

Modal: If I used C Major I'd be Playing, D Dorian, G Mixolydian, and C Ionian. Hm,
I want to sub Galt over the G7 (the 7th mode of Ab melodic minor). Maybe over the
Dm perhaps D melodic minor or D Aeolian (6th mode of F major)
I know what you mean,it is not enough just to be able to play modes up and down. You have to memorize the sound of each mode. You have to be able to hear a lick or song and identify what mode its in. Then when your hear V chord, you already have an idea what the mixolydian licks sound like so you just play what you hear in your head!

Okay, a mode of the major scale contains the same notes as the major scale, but the root is a different note. This is just explaining where modes come from, but I don't think of them like this when actually using them.
D Ionian (major) is D E F# G A B C#
E Dorian (second mode) is E F# G A B C# D
A mixolydian (fifth mode) is A B C# D E F# G
They contain the same notes but start on different root notes.

So, they contain the same notes but they are definately different scales. I think of modes as alterations to the major scale.
Ionian (Major) 1 2 3 4 5 6 7
Dorian 1 2 b3 4 5 6 b7
Phrygian 1 b2 b3 4 5 b6 b7
Lydian 1 2 3 #4 5 6 7
Mixolydian 1 2 3 4 5 6 b7
Aeolian (Natural Minor) 1 2 b3 4 5 b6 b7
Locrian 1 b2 b3 4 b5 b6 b7

So, for F Phrygian you start with the F major scale, F G A Bb C D E
Then flatten the 2 3 6 and 7 to get 1 b2 b3 4 5 b6 b7
And you end up with the notes F Gb Ab Bb C Db Eb.

Now, when playing modes over chords, look at the intervals making up the chord and the intervals making up the mode. If they match up, they will sound good together.
Say a Cm chord comes up, thats 1 b3 5. Look at the modes and you see that Dorian, Phrygian and Aeolian all contain those intervals.
So you could play C Dorian, C Phrygian or C Aeolian, which one you chose will give a different feel.
Now if an Amaj7 comes along, thats 1 3 5 7. Compare that to the modes and you see that you can play A Ionian or A Lydian, againg giving different feels.
What about a Bbm7b5? You see that the only mode with 1 b3 b5 b7 is Locrian, so you can play Bb Locrian
With an E7 (1 3 5 b7) you find that only Mixolydian fits, so you can play E mixolydian

JohnlJones Jazz-Theory Bit:
With that E7 you could play E Phrygian, with the b3 funtioning as a #2, to outline an altered dominant chord.
E7 - 1 3 4 b7
E Phrygian 1 b2 b3 4 5 b6 b7
This gives the intervals 1 b2 #2 3 4 5 b6 b7 which is a _11b9#9b13 chord.

Remember none of this is law, it's just a guide so don't be afraid to experiment.
Hope this helps

The way to use modes and get their different sounds is to think of the intervals it is made up of. Phrygian has a b2, a dark, dissononant interval. Lydian has a #4, which sounds... I dunno how to describe it but it sounds cool. Mixolydian is like the major scale but has a b7, making it bluesy and dominant.

Just drone the low E string, keep it ringing (clean setting works best). Then on the remaining five stings, play E Phrygian, E lydian, E Aeloian, E Ionian etc. and emphasise the unique intervals in each. Really listen to each scales' characteristics. Try making a melody from each mode while droning the E string.

Once you have done this, watch this video:
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and got a little queestion modes only can be made with the major scale or you could use them with the pentatonic or anything else