What are some alternatives?
When comparing MkDocs and Doxygen, you can also consider the following products
GitBook - Modern Publishing, Simply taking your books from ideas to finished, polished books.
ReadTheDocs - Spend your time on writing high quality documentation, not on the tools to make your documentation work.
Sphinx Search - Sphinx is an open source full text search server, designed with performance, relevance (search quality), and integration simplicity in mind. Sphinx lets you either batch index and search data stored in files, an SQL database, NoSQL storage.
Slate API Docs Generator - Create beautiful, intelligent, responsive API documentation.
Daux.io - Daux.io is a documentation generator that uses a simple folder structure and Markdown files to...
Natural Docs - Natural Docs is an open-source documentation generator for multiple programming languages.