Tree *AllocateTree (int numTaxa, int isTreeRooted);
int	  DerootTree (Tree *t, int outgroup);
int   DoMcmc (void);
int   DoMcmcp (void);
int   DoMcmcParm (char *parmName, char *tkn);
int   DoReassemble (void);
int   DoReassembleParm (char *parmName, char *tkn);
void  FreeTree (Tree *t);
void  GetDownPass (Tree *t);
int	  MoveCalculationRoot (Tree *t, int outgroup);
FILE *OpenNewMBPrintFile (char *fileName);
int	  RootTree (Tree *t);
void  SetBit (int i, long *bits);
void  SetUpMoveTypes (void);