ReadMatrix* read;
FullMatrix* matrix;
GroupMap* groupMap;
- string filename, format, method;
- string phylipfile, columnfile, namefile, groupfile;
+ string distFileName, format, method;
+ string phylipfile, columnfile, namefile, groupfile, outputDir;
NameAssignment* nameMap;
- OptionParser* parser;
- map<string, string> parameters;
- map<string, string>::iterator it;
- bool abort;
+
+ bool abort, sim, hard;
};