upgraded to rails 4.1.4 and mysql to 2.9.1
added test files in and output to fixtures folder
replaced "EPAWebserver::Application" with "Rails.application"
raxml_controller:
  -the directory name is added to the raxml model, but the actual
directory is only created when the form had no errors
  Raxml.find has changed for the new rails version; use of find_by
views/raxml/submit_single_gene.erb: started reworking of the select
options, which are not displayed anymore, since the assembled strings
"<option>1</option>" are escaped to be normal characters with newer
versions of rails, and a better way should be used to create the select
fields