At present pregap4 and gap4 clearly show their primary usage in the field of genome assembly, but versions tailored to mutation studies can be created once the requirements are agreed. Ideally all processing should be controlled by a single program which once configured for any project should require users to provide only the project name - all other file names and parameters could be preset, and all processing, including archiving and backup, performed automatically, leaving the data ready for visual inspection.
The automatic mutation and heterozygote detection programs work well on all the test data we have but now they require evaluation by external groups. Such analysis would enable us to improve the algorithms and to tune their parameters. At present we know that sometimes a base will be declared both as a mutation and as a heterozygous position when visual inspection shows that it is one or the other.
There is still much that can be done overall to improve the methods, but the text above summarises their status in July 2002. Although currently valuable for real scientific and clinical work they should perhaps be viewed as prototypes.