Major Refactoring

Loads of changes (143 commits)...

Changes include:

* Update Readme
* Remove un-needed files
* Update Test Units
* Update Travis so it installs mafft
* Update dependencies
* Add warning modal if not using firefox and the protocol is `file://`
* Add Approach, Explanation and Conclusion 
* Minor UI Changes - button like hover effect
* general refactoring all over...