The option was renamed from "dependencyTree" to "parseFile". This
should work:
"bin/x86_64/extractDependencyCounts.x86_64-standard --parseFile
e.parse.gz --leftOut e.counts.left.3gram.gz --rightOut e.counts.right.
3gram.gz --headOut e.counts.head.gz"
Sorry, we will update it in the manual and usage.