The Parameters Tab is organized as three sub-tabs: Input, Computation and Output (Figure 12). The input parameters and output data options that can be specified are different for the Genomic and cDNA sequence types. Each sequence type will have its own set of parameters under the project sub-tabs.

For a new project, the assembly parameters that take numerical values are initially set with their default values, as shown. If an invalid value is entered into any of these fields, a small red “X” appears in the lower left corner of the field and activates the “Not ready for analysis” warning in the upper right hand corner of the screen. Pausing the mouse over the red X reveals a tooltip indicating the allowed values for the parameter (see Section 1.12).