ATQA is not include as part of the Staden package. It is available from its developers, Daniel H. Wagner, Associates, at http://www.wagner.com/
score = -10*log10(probability of error).(This is the same log scale used by Phred.) In fact, the ATQA program computes four confidence values for each called base. The first three values correspond to the probabilities of substitution, insertion, and deletion errors, respectively. The fourth value is a combined score representing the probability that the called base is an error of any sort. Currently, only the combined confidence value is used by Staden package software.
Unlike Phred, the ATQA program does not produce base calls. Rather, it assigns confidence values to each base call in a lane file based on features of the trace data. The current version of the ATQA program is tuned to base calls made by the ABI base caller and to trace data from the ABI 377 sequencer.
Although ATQA can read ABI files, it will not create SCF files in such circumstances. However pregap4 will always convert any non SCF trace files into SCF format before running ATQA, so an explicit conversion is not required.