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There are several Linux solutions to show beamer presentations listed here:

Is there a nice solution to get a "presenter mode" for Latex presentations?

However, all of them use fullscreen mode. I am looking for one where presentation and notes are shown in two separate windows. The reason is that I would like to present over video conferencing software and share presenter window only while keeping notes on my screen.

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    As answered to the question Is there a specialized Pdf viewer for Latex-Beamer presentations on Linux?, take a look at pdfpc – Hafid Boukhoulda Dec 8 '18 at 6:46
  • It is the different question. I am looking for one which uses windows not screens. pdfpc, as many other viewers listed there do not use windows. – krokodil Dec 9 '18 at 0:00
  • Does your video conferencing software allow to share a region of your screen? What I normally do is to open a pdf which has presentation and notes on the same page besides each other with an ordinary pdf viewer and only share the area where the presentation slide is visible. – user36296 Dec 9 '18 at 14:40
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pympress is multi-platform and uses two windows which you can both put in fullscreen mode or keep windowed. I've successfully broadcast my content window (slides) on twitch while keeping the presenter window (notes) to myself, using Streamlabs OBS. I'm not sure which video conferencing software you are using but it should work fine as well.

Disclaimer : I am the maintainer of pympress.

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    this is what I ended up using. – krokodil Jun 8 at 1:59

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