cap3: the executable code of CAP3 program. Type cap3 for usage.

formcon: the executable code of FORMCON program
         for generating a constraint file for CAP3. Type formcon for usage.

doc: document for CAP3 and FORMCON

aceform: a specification of the ace file format

Note that CAP3 can be used in a similar way as Phrap, where
Phred is used for base calls, CAP3 for assembly, and Consed for
viewing ace format output of CAP3.

For questions on CAP3, please contact Xiaoqiu Huang at xqhuang@cs.iastate.edu