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You need to know some computer stuff (I am intentionally broad) to solve this one.

Were you a mod, you would see my dead peer;
The opposite tree I try to make clear.
When you read between lines, the answer is near;
If you don't, I am hidden forever, I fear.

Who am I?

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I’m not sure about posting this as an answer, since you are clearly

a (HTML) comment.

If I were a mod,

I could see deleted comments on SE

The opposite tree refers to

the DOM tree (letters of ”mod” reversed), which contains the document’s structure. A comment’s job is often to make that structure easier to understand.

When I read between the lines

of the source code to this puzzle, I notice that there is actually a html comment between lines 1 and 2,

Which is, of course hidden, (or invisible as the title suggests) unless I do exactly that.

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May be i am over thinking, But this also fits.

You are a

Network

Were you a mod, you would see my dead peer;

mod can be modem. So if i were a modem, i could see the dead peer(dead device) in you (Using Dead peer detection)

The opposite tree I try to make clear.

This can be EERT[Energy Efficient Reliable Transport]. EERT is a proposed method for better data delivery ratio in network communication. So "I try to make clear" is making sense here.

Last two lines.

I think those are just to tell to concentrate on the lines(first two) to get the correct answer. Otherwise nobody would be able to find the answer.

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