Assuming you have downloaded the whole repository, proceed as follows:
cd trunk/public/analysis make evalwikiopt cd ../../research/trust-analysis make evalwikiopt
This produces, in trunk/research/trust-analysis, a version of evalwiki with an extended set of command-line options. Do ./evalwiki -help for a list of the command line options available in the research version of the tool.
UCSC WikiLab Wiki