int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
int findRoot(); //return index of root node
//this function takes the leaf info and populates the non leaf nodes
map<string, int>::iterator it, it2;
map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
map<string, int>::iterator it, it2;
map<string, int> mergeGroups(int); //returns a map with a groupname and the number of times that group was seen in the children
void printBranch(int, ostream&, string); //recursively print out tree
void parseTreeFile(); //parses through tree file to find names of nodes and number of them
//this is required in case user has sequences in the names file that are
//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.
void printBranch(int, ostream&, string); //recursively print out tree
void parseTreeFile(); //parses through tree file to find names of nodes and number of them
//this is required in case user has sequences in the names file that are
//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.