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I would like to use some of theese greek fonts in LyX for my thesis: http://aka-acid.com/fontsscript.html

I installed the theme but I don't know how to use it in LyX

I also installed XeTeX

Can someone who uses LyX, guide me step by step?

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By 'theme' do you mean the font? (And, as an aside, I would beseech you not to use these fonts in your thesis... it is your decision of course, but imho they don't look professional.) –  Sean Allred Aug 5 '13 at 17:41
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I am not an expert but I just spent a lot of time figuring this out myself.

In LyX go to document settings. Under fonts, check use XeTeX fonts, and pick your fonts. You should be good to go.

If you want, or that doesn't work, you can also put the following in your preamble:

\setmainfont{nameofyourinstalledfont} %set font for main document

This will override the setting above.

If you want to change this at any time in your document, just insert an ERT with:

\setmainfont{nameofnewinstalledfont} %set new font for main document

You can also use fontspec e.g. \fontspec[Numbers=OldStyle]{Bergamo Std}

It depends on where you want to go...

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