Start the program
--------------------
If you have followed the installation instructions, see doc/install.txt, 
you can start the editor by simply writing SARSE whereever you are.

The program takes 2 commandline parameters
--file=filename
	The file you want to use in a new project. 
	Don't use ~ in the path, use absolute paths 

--project=projectname
	The existing project you want to use

--project and --file=filename
	If you use both parameters together, a new project will be created using the 
	file and the projectname, and will be located in the current directory. In this
	way no further clicking is needed to start working.


Open file/New Projects
--------------------------------
Sarse is project oriented which means that every time you open a file
a project must be created. 

File -> New

This opens a dialog where you are requested to select the file you want to open.
When you press 'Open' you are asked for a name to the project and a working directory. 
Defaults are provided, default projectname is the name of the file without the 
filetype-postfix(eg. '.col'). Default working directory is the directory from which 
you started Sarse. You can accept the defaults or give new ones of your liking.
If appropiate the file will be copied to the working directory.

Example: You start a project with a file named HIV1-leader2.txt then the default project
name is HIV1-leader2


Open an existing project
------------------------
If you want to open an existing project, 
File -> Open project

Then you get a list of existing projects where you can choose the name of the project you 
want to open


Delete a project
----------------
If you have a project you don't want to work on again delete it

File -> Delete Project

Then you get a list of all your projects and you can choose which one to delete.
You can only delete 1 project at a time, and it is not allowed to delete an open project.


Save file in another location / Export
--------------------------------------
If you want to save your alignment outside Sarse f.x. if you wan't to use it in another program
or want a fasta file
File -> Export File

Then you select a location, writes a filename and selects a format.


Delete sequences
----------------
Select the names of the sequences you wan't to delete, to the left on the screen.


Move bases
------------
You can move the bases in the alignment as long as there are a gab to move it into.
Select the bases you want to move by left-clicking and dragging. Then move the bases
by dragging the selection while holding the right mouse-button down.
