int         AddString (char ***list, int len, char *token);
SafeLong    Expecting (int y);
int         CheckString (char **list, int len, char *token, int *matchIndex);
int         CheckStringValidity (char *s);
int         DoExecute (void);
int         FreeMatrix (void);
int     	GetToken (char *token, int *tokenType, char **sourceH);
int      	FindValidCommand (char *tk, int *numMatches);
int         IsArgValid (char *s, char *validArg);
int         IsIn (char ch, char *s);
int         IsSame (char *s1, char *s2);
int         IsWhite (char c);
int         ParseCommand (char *s);
void        ResetCharacterFlags(void);
void        ResetTaxaFlags(void);
int         RootUserTree (TreeNode *p);
void        SetUpParms (void);
void     	ShowNodes (TreeNode *p, int indent, int isThisTreeRooted);
int      	ShowTree (Tree *t);
void        State_CODON (char *state, int code, int division);
void        State_DOUBLET (char *state, int code);
int			StateCode_AA (int n);
int			StateCode_NUC4 (int n);
int			StateCode_Std (int n);
char     	WhichNuc (int x);