- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it4;
- bool abort;
- string groups, itersString;
- vector<string> Groups; //holds groups to be used
+ bool abort, phylip, random, includeRoot;
+ string groups, itersString, outputDir, outputForm;
+ vector<string> Groups, outputNames; //holds groups to be used
+ map<string, vector<string> > outputTypes;