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I have a journal article with citations in APA format (e.g. Coley et al 2004) and I need to convert them to the IEEE format (represented with numbers, such as [1]), which are then listed at the bottom of the document.

Is there a software that can do this automatically (any editor, Word, OpenOffice) or I have to do this manually reinserting them in Word through the Citations manager?

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I have never followed the IEEE style so I had to look it up.

The only way you can convert the style as far as I know is to do it manually. You can use Word's citation/bibliography manager if you wish. If IEEE style is not available in your copy of Word, there is an IEEE Reference Style file available here.

You can of course type the references manually, which may or may not be quicker. It depends on your experience.

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