#include "groupmap.h"
#include "validcalculator.h"
#include "tree.h"
-#include "treemap.h"
+#include "counttable.h"
#include "readmatrix.hpp"
#include "readcolumn.h"
#include "readphylip.h"
NameAssignment* nameMap;
ListVector* list;
- TreeMap* tmap;
+ CountTable* ct;
Tree* t;
InputData* input;
vector<Calculator*> treeCalculators;
vector<SharedRAbundVector*> lookup;
string lastLabel;
- string format, groupNames, filename, sharedfile, inputfile;
+ string format, groupNames, filename, sharedfile, countfile, inputfile;
int numGroups, subsampleSize, iters, processors;
ofstream out;
float precision, cutoff;