#define	STRING_LENGTH	6000

#define	DNA				0
#define	RNA				1
#define	PROTEIN			2
#define	RESTRICTION		3
#define	STANDARD		4
#define	MIXED			5

#define	POISSON			0
#define	EQUALIN			1
#define	JONES			2
#define	DAYHOFF			3
#define	GTR				4

#define	UNIV			0
#define	VERTMT			1
#define	MYCO			2
#define	YEAST			3
#define	CILIATES		4
#define	METMT			5

#define	ALL_COMPAT		0
#define	HALF_COMPAT		1

extern int    DerootTree (TreeNode *r);
extern int    Dex2 (TreeNode *p);
extern double EnterNum (void);
extern void   FinishTree (TreeNode *p, int *x, int isThisTreeRooted);
extern void   ParseCommand (char *s);
extern int    RootTree (TreeNode *p);
extern void   SetUpCommandHierarchy (void);
extern void   ShowNodes (TreeNode *p, int indent, int isThisTreeRooted);
extern void   SortVector (double *item, int count);
extern void   SortVector2 (double *item, int left, int right);