+ vector< map<float, float> > rScoreFreq; //map <weighted score, number of random trees with that score.> -vector entry for each combination.
+ vector< map<float, float> > rCumul; //map <weighted score, cumulative percentage of number of random trees with that score or higher.> -vector entry for each c
+ map<float, float> validScores; //map contains scores from random
+
+ bool abort, phylip, random, includeRoot, subsample, consensus;
+ string groups, itersString, outputForm, treefile, groupfile, namefile;
+ vector<string> Groups, outputNames; //holds groups to be used
+ int processors, subsampleSize, subsampleIters;
+ ofstream outSum;
+ map<string, string> nameMap;