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It's hard to be too specific without seeing your writing, and I certainly have nothing close to an algorithm for you, but I was caught by your idea of reverse-engineering an outline. Does that mea...
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#3: Attribution notice added
Source: https://writers.stackexchange.com/a/2254 License name: CC BY-SA 3.0 License URL: https://creativecommons.org/licenses/by-sa/3.0/
#2: Initial revision
It's hard to be too specific without seeing your writing, and I certainly have nothing close to an algorithm for you, but I was caught by your idea of _reverse-engineering_ an outline. Does that mean that you didn't write from an outline to begin with? If so, and if you're having trouble with organization (as I assume you are, since you mention order, topic sentences and transitions), then I'd strongly recommend that you START with an outline, and THEN write your paper. If you already have all of your ideas, evidence, etc. set up in the outline, then you just need to base your work off that and your organization should almost take care of itself. Maybe I've misinterpreted, and you outline, write, and then re-outline? I'm not sure, but I'd definitely recommend an outline as the first step for anyone struggling with organization.