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TeX and LaTeX. Still the best software available to translate structured markup to a pdf.

If you are doing anything with equations, LaTeX is definitely the way to go. Unfortunately, it's a steep learning curve for regular ebooks.

The downside is it's not super HTML-friendly (there are converters, but you can't display equations easily in HTML) so converting to Mobi, ePub, etc. is not straightforward.

Certainly it has a steep learning curve but it has a very large community that supports its packages and now also has a friendly and helpful community http://tex.stackexchange.com/

They can be as friendly and helpful as you want, but that doesn't change the fact that the input format for mobi and epub is basically HTML; meaning that by utilizing TeX, you are basically adding another layer that doesn't provide much value. The beautiful fonts, formatting, spacing, etc.. etc... that TeX provides will all be lost on your ereader.

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