This quick tour just gives a brief introduction to the some often used features in CodonCode Aligner. For a more complete description of Aligner features, you should use Aligner's online help. You can access Aligner's online help from within Aligner (we'll show you in a minute), or use the "AlignerHelp.pdf" file that was installed in your CodonCode Aligner directory when you installed Aligner.
To use the online help from within CodonCode Aligner, open Aligner, and then choose "Aligner Help..." from the "Help" menu (or press the F1 key). This will open a new help window like this one:
The help is context-sensitive, and Aligner will try to show you a help item that relates to the window which was in the foreground when you opened the help. If the project view was active, the explanation of the project view shown above will be displayed.
You can use the topic list on the left side to quickly move around in the help. For example, click on the triangle before "Editing Samples" to view the related topics, and look at a few of them. If you are looking for something specific, you can also use the index or the search functions, as described next.
To view a keyword index of Aligner help topics, click on the middle tab on the top left side (where the cursor is in the image below).
Clicking on any keyword on the left will show the corresponding page on the right - try it out!
If you are looking for something specific, you can use the Search function in the online help. Click on the tab that has the little magifying glass, enter a search string (for example "quality"), and press the return key. Aligner will show you a list of pages that contain all or some of your search term, ranked by significance. Clicking on any of the results will take you to the corresponding help page, as shown below:
If you are just want to know more about a specific menu item, for example "Clip Ends..." in the "Sample" menu, the fastest way to find out more is to go back to the table of contents in the online help (the left-most tab that shows a little book), and click on the item "Help by Menu" (you may need to scroll down a bit). This shows help for all menues and menu items:
Clicking on the menu name will bring you to the help for the menu items, and then clicking on the menu item will show the relevant help page. Try it by clicking on "Sample" (or "Sample Menu" on the left tab), and then on "Clip Ends...". This will show the help page that describes end clipping.
We recommend that you (at least) browse through the online help when you start to use CodonCode Aligner, and whenever something does not work the way you think it should. Chances are pretty good that you will learn something useful (but should you find something that is unclear, missing, or wrong in the help, please let us know).
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