TreeMap* getTreeMap() { return tmap; }
void getCopy(Tree*); //makes tree a copy of the one passed in.
+ void getCopy(Tree* copy, map<string, string>, vector<string>); //makes a copy of the tree passed in, but everyone who is not in the vector<string> has group set to doNotIncludeMe. Assumes the tmap already has these seqs group set to doNotIncludeMe.
void getSubTree(Tree*, vector<string>); //makes tree a that contains only the names passed in.
int getSubTree(Tree* originalToCopy, vector<string> seqToInclude, map<string, string> nameMap); //used with (int, TreeMap) constructor. SeqsToInclude contains subsample wanted - assumes these are unique seqs and size of vector=numLeaves passed into constructor. nameMap is unique -> redundantList can be empty if no namesfile was provided.