Create fileCopy.jsp

Server page that creates and writes the modified alignment file on the server before sending it to the client. This server page is used in the table mode visualization.
Create treeCopy.jsp

Server page that creates and writes the modified alignment file on the server before sending it to the client. This server page is used in tree mode visualizations.
Update README.md
Merge pull request #1 from VAlbir/src

Src