Commonly Used BaseFinder Tools and Typical Parameter Values
| Tool name | Tool function | Typical parameter values |
| ToolDeletePrimer2 | deletes all data before dye primer | none |
| FittedBaselineAdjust | removes baseline drift | width = 75 |
| ToolMatrix2 | transforms data from spectral to dye concentration | matrix appropriate for dye and instrument combination |
| ToolConvolve | smooths data to reduce noise | ς = 1.5;M = 10 |
| DeconvolutionTool | improves resolution by reducing band spreading | iterations = 5, α = 0.25, spread function polynomial based on typical data |
| ToolManualDeletion | removes selected regions of data, e.g., at end or beginning | none |
| ToolMobility3 | corrects polynomials for data shifts due to dye mobility differences | shift values appropriate to dye set |
| ToolNormalize2 | normalizes peak heights | none |
| ToolCutoffHisto | Removes highest and lowest points from the data to improve normalization | threshold = 2% |
| ToolBaseCalling | labels peaks with base-calls | see text |