Annotation for pdf

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Okular works best for pdf's in Ubuntu. It's got great features and that  
should be suffice. However, the annotations that you do are limited for  
viewing by okular.

If you want a better solution try out Xournal. It's not exactly a pdf  
annotation tool but that should not worry you. Foxit Linux is useless  
bundle not even worth for free. If you have a lot of research articles,  
look no further than Mendeley. That annotates (sticky notes) and  
highlights in equal measure.

Hope that helps.