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How to set up LyX under Windows to use it for Lithuanian
Problems with default settings
By default LyX uses the TeX fonts to create the PDF output. The disadvantage is that these fonts cannot handle Unicode. Therefore your document might look good if you have for example used the Latin Modern fonts but if you copy text in the PDF and paste it to a text editor you will see that for example "Rytų Prūsijoje" is pasted as "Rytu Prusijoje". This is because Latin Modern does not contain the characters that include accents.
The solution is to use non-TeX fonts. To do this check in the menu Document→Settings→Fonts the option Use non-TeX fonts. The default font delivers already a nice and correct result but you are of course free to choose another font.