Please use the following reference:

Machado, M., Magalhaes, W., Sene, A., Araujo, B., Faria-Campos, A., Chanock, S., Scott, L., Oliveira, G., Tarazona-Santos, E., and Rodrigues, M. (2011). Phred-phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies. Investigative Genetics, 2(1), 3.
Open access pdf.