To run CAP3 on Windows, you need to download CYGWIN,
a Linux similator on Windows at http://www.cygwin.com,
and run CAP3 on CYGWIN.


doc: document for CAP3 and FORMCON

aceform: document on .ace format.

example: a directory with a small data set

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
