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I wrote:

They each belong to a different node. To distinguish them, the node index together with the variable is stored in the list.

Is it correct? How about

They each belong to a different node. To distinguish them, the node index is stored in the list, together with the variable

or even:

They each belong to a different node. To distinguish them, together with the variable, the node index is also stored in the list.

I mean to distinguish two variables with the same name where each belongs to a different node, the node index is stored together with each variable.

Actually I don't know the position of together with variable in this sentence. Should it immediately follows the name with which it comes or it can be after the verb?

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    All three are fine, though the first should have commas around the phrase in bold. The only caveat is that I'm not sure what you're distinguishing. If the sense of your sentences remains the same with the parts in bold deleted, then your constructs are all fine. Otherwise, you'll need to edit to explain what you intended to 'distinguish them' with. – Lawrence Oct 6 '16 at 17:04
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    All of them are acceptable, although I don't like the third one very much because putting the adverbial phrase "together with the variable" before the thing it actually applies to makes the sentence read less clearly - it looks like "together with the variable" is applying to "to distinguish them". – stangdon Oct 6 '16 at 18:18
  • @Lawrence I edited the question. – Ahmad Oct 6 '16 at 19:28
  • The node index is stored together with the variable in that list. – Tᴚoɯɐuo Oct 6 '16 at 20:37
  • @Ahmad Then they're fine, but consider clarifying: "We store the node index with the variable to disambiguate identically-named variables." – Lawrence Oct 6 '16 at 23:47
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The collocation together with takes a nominal complement. That together-with phrase, together with {something} is adverbial, expressing manner, and therefore readily follows immediately after the verb; assuming that the "variable" in question has been mentioned in the preceding sentence, we could write:

To distinguish them, the node index is stored, together with that variable, in the list.

It seems the list was also previously mentioned, to judge from the definite article, though it would be better if the list hadn't been mentioned until this sentence:

To distinguish them, the node index is stored, together with that variable, in a list.

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