All the functionality of ChemTree can be conceptually organized in a framework of activities that have to be performed each time you use the program. We call the framework the ChemTree basic workflow and it consists of the following activities:

1. Create a new ChemTree project (or open an existing project).
2. Import one or more data sets into the project.
3. View the imported data in a Spread Sheet Viewer.
4. In the Spread Sheet Viewer identify the specific data rows and columns that are to be used in analysis.
5. Perform the analysis.
6. Export the results of the analysis for publishing.

ChemTree can be executed in either GUI mode or scripting mode. The GUI mode allows for a ’hands-on’, interactive use of the tool and the scripting mode allows the tool to be used in a ’hands-off’, batch oriented fashion.

The following two tutorials provide a concrete illustration of performing the basic workflow. The first tutorial leads you through the basic workflow for ChemTree in GUI mode. The second tutorial demonstrates how the Cherry Picking module works in ChemTree.