To create a new project, open CodonCode Aligner, go to the "File" menu, and select "New Project".
If you selected to set the project path when creating new projects (in the "Open & Save" preferences), Aligner will first will show a standard "Save As" file dialog, allowing you to pick the name and location for your project; this was the default behavior in Aligner before version 1.1.5.
Aligner will open a new project view window, showing the (empty) "Unassembled Samples" and "Trash" folders:
Aligner will save changes to projects only if you explicitely tell it to. To save your new project, go to the "File" menu and choose "Save Project". Alternatively, you can use the "Save Project" button in the toolbar in the project view, or the keyboard shortcut (Command-S on OS X, Control-S on Windows).
Unless you already specified the project name and location when creating a new project, Aligner with show a standard "Save As" file dialog, allowing you to pick the name and location for your project.
After you saved your project, you will notice that the "Save Project" menu item becomes unavailable. It will become available again as soon as you make changes to your project, for example by adding samples.
CodonCode Aligner saves all data for a project inside a directory with the name of the project. This directory contains one or more sub-directories, the project file (which has the name of the project with ".proj" appended), and a couple of other files for status messages and project locking.
When working with CodonCode Aligner, it is important that you save your changes on a regular basis. Sometimes, you may want to use the "Save As..." command in the "File" menu to save the project under a different name, basically creating a copy of the project. This allows you to experiment with different settings, and compare the results by looking at the different copies.
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