4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
6 #ifndef ROOTEDCLUSTERTREE_H
7 #define ROOTEDCLUSTERTREE_H
8 #include "../ClusterTree.h"
9 #include "RootedGuideTree.h"
10 #include "../AlignmentSteps.h"
14 class RootedClusterTree : private ClusterTree
17 //RootedClusterTree();
19 * NOTE these will have different signatures!!!!
21 void treeFromAlignment(TreeNames* treeNames, Alignment *alignPtr);
22 auto_ptr<AlignmentSteps> treeFromDistMatrix(RootedGuideTree* phyloTree,
23 DistMatrix* distMat, Alignment *alignPtr, int seq1,
24 int nSeqs, string& phylipName);