int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
- void assembleTree();
+ int assembleTree();
vector<Node> tree; //the first n nodes are the leaves, where n is the number of sequences.
//not included in the tree.
//only takes names from the first tree in the tree file and assumes that all trees use the same names.
int readTreeString(ifstream&);
+
+ MothurOut* m;
};