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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifndef ROOTEDCLUSTERTREE_H
#define ROOTEDCLUSTERTREE_H
#include "../ClusterTree.h"
#include "RootedGuideTree.h"
#include "../AlignmentSteps.h"
namespace clustalw
{
class RootedClusterTree : private ClusterTree
{
public:
//RootedClusterTree();
/**
* NOTE these will have different signatures!!!!
*/
void treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr);
auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
DistMatrix* distMat, Alignment *alignPtr, int seq1,
int nSeqs, string& phylipName);
};
}
#endif
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