Adobe InDesign for Media and Publishing
As Adobe InDesign was originally used as a print-centric program and was upgraded to be more conducive for digital publishing. Some of the formats InDesign uses to publish is EPUB, Adobe Digital Publishing Suite (DPS), and Interactive PDFs.
In an article by Digital Publishing 101, mentions InDesign is easier to be exported for Kindle ebooks using a free Amazon plugin since the only format Kindle uses is MOBI, and DPS aids in distribution of publication as an apps. Apps have made ebooks more accessible with the use of tablets and smart phones.
EPUB is probably the most common format used in publishing. EPUB was originated by the International Digital Publishing Forum (IDPF) and is an open standard. EPUB3 was recently introduced to give more interactive flexibility to the types of various publications.