With MathType you can insert equations as EPS images into InDesign. Using EPS images will allow InDesign to display the equations nicely no matter what form of output you choose.
InDesign is a desktop publishing application produced by Adobe.
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MathType is a powerful interactive equation
editor for Windows and Macintosh that lets you create mathematical notation
for word processing, web pages, desktop publishing, presentations,
elearning, and for TeX, LaTeX, and MathML documents. 