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diff --git a/amovacommand.h b/amovacommand.h
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+#ifndef AMOVACOMMAND_H
+#define AMOVACOMMAND_H
+
+/*
+ *  amovacommand.h
+ *  mothur
+ *
+ *  Created by westcott on 2/7/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "command.hpp"
+class GroupMap;
+
+class AmovaCommand : public Command {
+	
+public:
+	AmovaCommand(string);
+	AmovaCommand();
+	~AmovaCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "amova";					}
+	string getCommandCategory()		{ return "Hypothesis Testing";		}
+	string getHelpString();	
+	string getCitation() { return "Anderson MJ (2001). A new method for non-parametric multivariate analysis of variance. Austral Ecol 26: 32-46.\nhttp://www.mothur.org/wiki/Amova"; }
+	string getDescription()		{ return "analysis of molecular variance"; }
+	
+	int execute();
+	void help() { m->mothurOut(getHelpString()); }
+	
+private:
+	double runAMOVA(ofstream&, map<string, vector<int> >, double);
+	double calcSSWithin(map<string, vector<int> >&);
+	double calcSSTotal(map<string, vector<int> >&);
+	map<string, vector<int> > getRandomizedGroups(map<string, vector<int> >);
+
+	bool abort;
+	vector<string> outputNames;
+
+	string outputDir, inputDir, designFileName, phylipFileName;
+	GroupMap* designMap;
+	vector< vector<double> > distanceMatrix;
+	int iters;
+	double experimentwiseAlpha;
+};
+
+#endif
+