- map<string, float> WScore; //a score for each group combination i.e. AB, AC, BC.
+ map<string, double> WScore; //a score for each group combination i.e. AB, AC, BC.
+ int processors;
+ string outputDir;
+ map< vector<string>, set<int> > rootForGrouping; //maps a grouping combo to the root for that combo
+ bool includeRoot;
+
+ EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*);
+ EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
+ double getLengthToRoot(Tree*, int, string, string);