void help();
private:
+ struct linePair {
+ int start;
+ int num;
+ linePair(int i, int j) : start(i), num(j) {}
+ };
+ vector<linePair*> lines;
+
GlobalData* globaldata;
SharedUtil* util;
FileOutput* output;
bool abort, phylip, random;
string groups, itersString;
vector<string> Groups, outputNames; //holds groups to be used
+ int processors;
ofstream outSum;
//void removeValidScoresDuplicates();
int findIndex(float, int);
void calculateFreqsCumuls();
+ int createProcesses(Tree*, Tree*, vector< vector<string> >, vector<double>&, vector< vector<double> >&);
+ int driver(Tree*, Tree*, vector< vector<string> >, int, int, vector<double>&, vector< vector<double> >&);
};