text: extern int intlen( int *num );
  extern char seqcheck( char **seq );
  extern void scmx_calc( int icyc, char **aseq, double *effarr, float **scmx );
  extern void exitall( char arr[] );
  extern void display( char **seq, int nseq );
  extern void intergroup_score( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
  extern void intergroup_score_gapnomi( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
  extern void intergroup_score_new( char **seq1, char **seq2, double *eff1, double *eff2, int clus1, int clus2, int len, double *value );
  extern double score_calc5( char **seq, int s, double **eff, int ex );
  extern double score_calc4( char **seq, int s, double **eff, int ex );
  extern void upg2( int nseq, double **eff, int ***topol, double **len );
  //extern void veryfastsupg_float_realloc_nobk_halfmtx( int njob, float **mtx, int ***topol, float **len );
  //extern void veryfastsupg_float_realloc_nobk( int njob, float **mtx, int ***topol, float **len );
  extern void veryfastsupg_int_realloc_nobk( int njob, int **mtx, int ***topol, double **len );
  extern void veryfastsupg( int nseq, double **oeff, int ***topol, double **len );
  extern void veryfastsupg_double( int nseq, double **oeff, int ***topol, double **len );
  extern void veryfastsupg_double_loadtree( int nseq, double **oeff, int ***topol, double **len );
  extern void veryfastsupg_double_loadtop( int nseq, double **oeff, int ***topol, double **len );
  extern void veryfastsupg_int( int nseq, int **oeff, int ***topol, double **len );
  extern void fastsupg( int nseq, double **oeff, int ***topol, double **len );
  extern void supg( int nseq, double **oeff, int ***topol, double **len );
  extern void spg( int nseq, double **oeff, int ***topol, double **len );
  extern double ipower( double x, int n );
  extern void countnode( int nseq, int ***topol, double **node );
  extern void countnode_int( int nseq, int ***topol, int **node );
  extern void counteff_simple( int nseq, int ***topol, double **len, double *node );
  extern void counteff_simple_float( int nseq, int ***topol, float **len, double *node );
  extern void counteff( int nseq, int ***topol, double **len, double **node );
  extern float score_calc1( char *seq1, char *seq2 );
  extern float score_calcp( char *seq1, char *seq2, int len );
  extern float substitution_nid( char *seq1, char *seq2 );
  extern float substitution_score( char *seq1, char *seq2 );
  extern float substitution_hosei( char *seq1, char *seq2 );
  extern float substitution( char *seq1, char *seq2 );
  extern void treeconstruction( char **seq, int nseq, int ***topol, double **len, double **eff );
  extern float bscore_calc( char **seq, int s, double **eff );
  extern void AllocateTmpSeqs( char ***mseq2pt, char **mseq1pt, int locnlenmax );
  extern void FreeTmpSeqs( char **mseq2, char *mseq1 );
  extern void gappick_samestring( char *aseq );
  extern void gappick0( char *aseq, char *seq );
  extern void gappick( int nseq, int s, char **aseq, char **mseq2, 
  					 double **eff, double *effarr );
  extern void commongappick_record( int nseq, char **seq, int *map );
  extern void commongappick( int nseq, char **seq );
  extern double score_calc0( char **seq, int s, double **eff, int ex );
  extern void strins( char *str1, char *str2 );
  extern int isaligned( int nseq, char **seq );
  extern double score_calc_for_score( int nseq, char **seq );
  extern void floatncpy( float *vec1, float *vec2, int len );
  extern float score_calc_a( char **seq, int s, double **eff );
  extern float score_calc_s( char **seq, int s, double **eff );
  extern double score_calc_for_score_s( int s, char **seq );
  extern double SSPscore( int s, char **seq );
  extern double DSPscore( int s, char **seq );
  extern int searchAnchors( int nseq, char **seq, Segment *seg );
  extern char *progName( char *str );
  extern void dontcalcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
  extern void calcimportance( int nseq, double *eff, char **seq, LocalHom **localhom );
  extern void weightimportance2( int nseq, double *eff, LocalHom **localhom );
  extern void weightimportance4( int clus1, int clus2, double *eff1, double *eff2, LocalHom ***localhom );
  extern void extendlocalhom( int nseq, LocalHom **localhom );
  extern void extendlocalhom2( int nseq, LocalHom **localhom, double **mtx );
  extern int makelocal( char *s1, char *s2, int thr );
  extern void mdfymtx( char **pair, int s1, double **partialmtx, double **mtx );
  extern float score_calc( char **seq, int s );
  extern void cpmx_calc( char **seq, float **cpmx, double *eff, int lgth, int clus );
  extern void cpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus );
  extern void MScpmx_calc_new( char **seq, float **cpmx, double *eff, int lgth, int clus );
  extern void mseqcat( char **seq1, char **seq2, double **eff, double *effarr1, double *effarr2, char name1[M][B], char name2[M][B], int clus1, int clus2 );
  extern void strnbcat( char *s1, char *s2, int m );
  extern int conjuctionforgaln( int s0, int s1, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d );
  extern int fastconjuction( int *memlist, char **seq, char **aseq, double *peff, double *eff, char name[M][B], char aname[M][B], char *d );
  extern int fastconjuction_noname_kozo( int *memlist, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d );
  extern int fastconjuction_noname( int *memlist, char **seq, char **aseq, double *peff, double *eff, char *d );
  extern int fastconjuction_noweight( int *memlist, char **seq, char **aseq, double *peff, char *d );
  extern int conjuctionfortbfast( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char *d );
  extern int conjuctionfortbfast_kozo( double *tmptmp, char **pair, int s, char **seq, char **aseq, double *peff, double *eff, double *peff_kozo, double *eff_kozo, char *d );
  extern int conjuction( char **pair, int s, char **seq, char **aseq, double *peff, double *eff, char **name, char **aname, char *d );
  extern void floatdelete( float **cpmx, int d, int len );
  extern void chardelete( char *seq, int d );
  extern int RootBranchNode( int nseq, int ***topol, int step, int branch );
  extern void BranchLeafNode( int nseq, int ***topol, int *node, int step, int branch );
  extern void RootLeafNode( int nseq, int ***topol, int *node );
  extern void nodeFromABranch( int nseq, int *result, int **pairwisenode, int ***topol, double **len, int step, int num );
  extern void OneClusterAndTheOther( int locnjob, char **pair, int *s1, int *s2, int ***topol, int step, int branch );
  extern void makeEffMtx( int nseq, double **mtx, double *vec );
  extern void node_eff( int nseq, double *eff, int *node );
  extern int shrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink );
  extern int msshrinklocalhom( char **pair, int s1, int s2, LocalHom **localhom, LocalHom ***localhomshrink );
  extern int fastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink );
  extern int msfastshrinklocalhom( int *mem1, int *mem2, LocalHom **localhom, LocalHom ***localhomshrink );
  extern int TreeDependentIteration( int locnjob, char **name, int nlen[M], char **aseq, char **bseq, int ***topol, double **len, int alloclen, LocalHom **localhomtable, RNApair ***single, int nkozo, char *kozoarivec );
  extern void checkMinusLength( int nseq, double **len );
  extern void negativeMember2( int *mem, int *query, int locnseq );
  extern int *negativeMember( int *query, int locnseq );
  extern int IntExistsInVec( int query, int *vector );
  extern NodeInCub searchParent( int top, int ***topol, int Start, int End );
  extern void stopolInit( int n, Node *stopol );
  extern void treeCnv( Node *stopol, int locnseq, int ***topol, double **len, double **bw );
  extern int isLeaf( Node node );
  extern double syntheticLength( Node *ob, Node *oppositeNode );
  extern double calcW( Node *ob, Node *op );
  extern void calcBranchWeight( double **bw, int locnseq, Node *stopol, int ***topol, double **len );
  extern void branchWeightToPairWeight( int locnseq, int ***topol, double **pw, double **bw );
  extern void weightFromABranch_rec( double *result, Node *ob, Node *op );
  extern void weightFromABranch( int nseq, double *result, Node *stopol, int ***topol, int step, int LorR );
  extern void keika( char *str, int current, int all );
  extern double maxItch( double *soukan, int size );
  extern void calcNaiseki( Fukusosuu *value, Fukusosuu *x, Fukusosuu *y );
  extern Fukusosuu *AllocateFukusosuuVec( int l1 );
  extern Fukusosuu **AllocateFukusosuuMtx( int l1, int l2 );
  extern Fukusosuu ***AllocateFukusosuuCub( int l1, int l2, int l3 );
  extern void FreeFukusosuuVec( Fukusosuu *vec );
  extern void FreeFukusosuuMtx( Fukusosuu **mtx );
  extern int getKouho( int *kouho, int nkouho, double *soukan, int nlen2 );
  extern void zurasu2( int lag, int    clus1, int    clus2, char  **seq1, char  **seq2, char **aseq1, char **aseq2 );
  extern void zurasu( int lag, int    clus1, int    clus2, char  **seq1, char  **seq2, char **aseq1, char **aseq2 );
  extern int alignableReagion( int    clus1, int    clus2, char  **seq1, char  **seq2, double *eff1, double *eff2, Segment *seg );
  extern void blockAlign( int *cut1, int *cut2, double **ocrossscore, int *ncut );
  extern void blockAlign2( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut );
  extern void blockAlign3( int *cut1, int *cut2, Segment **seg1, Segment **seg2, double **ocrossscore, int *ncut );
  extern float A__align11( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch );
  extern float imp_match_out_scH( int i1, int j1 );
  extern void imp_match_init_strictH( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
  extern float imp_match_out_scQ( int i1, int j1 );
  extern float imp_match_out_scR( int i1, int j1 );
  extern void imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
  extern void imp_match_init_strictR( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
  extern void imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom );
  extern float MSalignmm( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, int *, int, int *, int headgp, int tailgp );
  extern float Lalignmm_hmout( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, float **map );
  extern float Lalign2m2m_hmout( char **seq1, char **seq2, char **seq1r, char **seq2r, char *dir1, char *dir2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, char *, char *, char *, char *, float **map );
  extern float MSalign11( char **seq1, char **seq2, int alloclen );
  //extern float rnalocal( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, RNApair **pair );
  extern float A__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *, int, int *, int headgp, int tailgp );
  extern float H__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
  extern float Q__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
  extern float Q__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2, int *gapmap1, int *gapmap2 );
  extern float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
  extern float R__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, char *gs1, char *gs2, char *ge1, char *ge2 );
  extern float A__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 );
  extern float D__align_gapmap( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int *gapmap1, int *gapmap2 );
  extern float translate_and_Calign( char **mseq1, char **mseq2, double *effarr1, double *effarr2, int clus1, int clus2, int alloclen );
  extern double Fgetlag( char  **seq1, char  **seq2, double *eff1, double *eff2, int    clus1, int    clus2, int alloclen );
  extern float Falign( char  **seq1, char  **seq2, double *eff1, double *eff2, int    clus1, int    clus2, int alloclen, int *fftlog, int *, int, int * );
  extern float Falign_udpari_long( char  **seq1, char  **seq2, double *eff1, double *eff2, int    clus1, int    clus2, int alloclen, int *fftlog );
  float Falign_localhom( char  **seq1, char  **seq2, double *eff1, double *eff2, int    clus1, int    clus2, int alloclen, LocalHom ***localhom, float *totalimpmatch, int *gapmap1, int *gapmap2, int *chudanpt, int chudanref, int *chudanres );
  extern float part_imp_match_out_sc( int i1, int j1 );
  extern float part_imp_match_out_scQ( int i1, int j1 );
  extern void part_imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1_kozo, double *eff2_kozo, LocalHom ***localhom, int forscore );
  extern void part_imp_match_init_strictQ( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom, int forscore );
  extern void part_imp_match_init( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, LocalHom ***localhom );
  extern float partA__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *, char *, char *, char *, int *, int, int * );
  extern float partQ__align( char **seq1, char **seq2, double *eff1, double *eff2, int icyc, int jcyc, int alloclen, LocalHom ***localhom, float *impmatch, int start1, int end1, int start2, int end2, int *gapmap1, int *gapmap2, char *, char *, char *, char *);
  extern float G__align11( char **seq1, char **seq2, int alloclen, int headgp, int tailgp  );
  extern float G__align11_noalign( int mtx[0x80][0x80], int penal, int penal_ex, char **seq1, char **seq2, int alloclen );
  extern float L__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
  extern float genL__align11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt );
  extern float genG__align11( char **seq1, char **seq2, int alloclen );
  extern float VAalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt );
  extern float suboptalign11( char **seq1, char **seq2, int alloclen, int *off1pt, int *off2pt, LocalHom *lhmpt )
  ;
  extern int fft(int n, Fukusosuu *x, int dum);
  extern void topolcpy( int s1[], int s2[], int *mpt1, int *mpt2 );
  extern void topolcat( int s1[], int s2[], int *mpt1, int *mpt2 );
  extern void topolsort( int m, int s[] );
  extern void topolswap( int s1[], int s2[], int *mpt1, int *mpt2 );
  extern void reduc( double **mtx, int nseq, int im, int jm );
  extern void  nj( int nseq, double **omtx, int ***topol, double **dis );
  extern void JTTmtx( double **rsr, double *freq, char locamino[26], char locgrp[26], int isTM );
  extern void BLOSUMmtx( int n, double **matrix, double *freq, char *amino, char *amino_grp );
  extern void putlocalhom2( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
  extern void putlocalhom_str( char *al1, char *al2, double *equiv, double scale, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
  extern void putlocalhom_ext( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
  extern void putlocalhom3( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
  extern void putlocalhom( char *al1, char *al2, LocalHom *localhompt, int off1, int off2, int opt, int overlapaa );
  extern char *cutal( char *al, int al_display_start, int start, int end );
  extern void ErrorExit( char *message );
  extern void strncpy_caseC( char *str1, char *str2, int len );
  extern void seqUpper( int nseq, char **seq );
  extern void seqLower( int nseq, char **seq );
  extern int getaline_fp_eof( char *s, int l, FILE *fp );
  extern int getaline_fp_eof_new(char s[], int l, FILE *fp);
  extern int myfgets(char s[], int l, FILE *fp);
  extern float input_new( FILE *fp, int d );
  extern void PreRead( FILE *fp, int *locnjob, int *locnlenmax );
  extern int allSpace( char *str );
  extern void Read( char name[M][B], int nlen[M], char **seq );
  extern void FRead( FILE *fp, char name[][B], int nlen[], char **seq );
  extern void kake2hiku( char *str );
  extern void readDataforgaln( FILE *fp, char **name, int *nlen, char **seq );
  extern void readData( FILE *fp, char name[][B], int nlen[], char **seq );
  extern void readData_pointer_casepreserve( FILE *fp, char **name, int *nlen, char **seq );
  extern void readData_pointer( FILE *fp, char **name, int *nlen, char **seq );
  extern void readData_pointer2( FILE *fp, int nseq, char **name, int *nlen, char **seq );
  extern void readData_varlen( FILE *fp, char **name, int *nlen, char **seq );
  extern int countATGC( char *s, int *total );
  extern void getnumlen( FILE *fp );
  extern void getnumlen_casepreserve( FILE *fp, int *nlenmin );
  extern void getnumlen_nogap( FILE *fp, int *nlenmin );
  extern void WriteGapFill( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq );
  extern void writeDataforgaln( FILE *fp, int locnjob, char **name, int *nlen, char **aseq );
  extern void writeData( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq );
  extern void writeData_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq );
  extern void readhat2_floathalf( FILE *fp, int nseq, char name[M][B], float **mtx );
  extern void readhat2_floathalf_pointer( FILE *fp, int nseq, char **name, float **mtx );
  extern void readhat2_float( FILE *fp, int nseq, char name[M][B], float **mtx );
  extern void readhat2_int( FILE *fp, int nseq, char name[M][B], int **mtx );
  extern void readhat2_pointer( FILE *fp, int nseq, char **name, double **mtx );
  extern void readhat2( FILE *fp, int nseq, char name[M][B], double **mtx );
  extern void WriteFloatHat2_pointer_halfmtx( FILE *hat2p, int locnjob, char **name, float **mtx );
  extern void WriteFloatHat2( FILE *hat2p, int locnjob, char name[M][B], float **mtx );
  extern void WriteHat2_int( FILE *hat2p, int locnjob, char name[M][B], int **mtx );
  extern void WriteHat2( FILE *hat2p, int locnjob, char name[M][B], double **mtx );
  extern void WriteHat2_pointer( FILE *hat2p, int locnjob, char **name, double **mtx );
  extern int ReadFasta_sub( FILE *fp, double *dis, int nseq, char name[M][B] );
  extern int ReadSsearch( FILE *fp, double *dis, int nseq, char name[M][B] );
  extern int ReadBlastm7( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
  extern int ReadBlastm7_scoreonly( FILE *fp, double *dis, int nin );
  extern int ReadBlastm7_avscore( FILE *fp, double *dis, int nin );
  extern int ReadFasta34noalign( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
  extern int ReadFasta34m10_nuc( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
  extern int ReadFasta34m10( FILE *fp, double *dis, int qmem, char name[M][B], LocalHom *localhomlist );
  extern int ReadFasta34m10_scoreonly_nuc( FILE *fp, double *dis, int nin );
  extern int ReadFasta34m10_scoreonly( FILE *fp, double *dis, int nin );
  extern int ReadFasta34( FILE *fp, double *dis, int nseq, char name[M][B], LocalHom *localhomlist );
  extern int ReadFasta3( FILE *fp, double *dis, int nseq, char name[M][B] );
  extern int ReadFasta( FILE *fp, double *dis, int nseq, char name[M][B] );
  extern int ReadOpt( FILE *fp, int opt[M], int nseq, char name[M][B] );
  extern int ReadOpt2( FILE *fp, int opt[M], int nseq, char name[M][B] );
  extern int writePre( int nseq, char **name, int nlen[M], char **aseq, int force );
  extern void readOtherOptions( int *ppidptr, int *fftThresholdptr, int *fftWinSizeptr );
  extern void initSignalSM( void );
  extern void initFiles( void );
  extern void WriteForFasta( FILE *fp, int locnjob, char name[][B], int nlen[M], char **aseq );
  extern void readlocalhomtable( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec );
  extern void readlocalhomtable2( FILE*fp, int njob, LocalHom **localhomtable, char *kozoarivec );
  extern void outlocalhom( LocalHom **localhom, int nseq );
  extern void outlocalhompt( LocalHom ***localhom, int n1, int n2 );
  extern void FreeLocalHomTable( LocalHom **localhomtable, int n ) ;
  extern void constants( int nseq, char **seq );
  extern void clustalout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, char *mark, char *comment, int *order, int namelen );
  extern void phylipout_pointer( FILE *fp, int nseq, int maxlen, char **seq, char **name, int *order );
  extern void writeData_reorder( FILE *fp, int locnjob, char name[][B], int nlen[], char **aseq, int *order );
  extern void writeData_reorder_pointer( FILE *fp, int locnjob, char **name, int *nlen, char **aseq, int *order );
  
  extern void resetlocalhom( int, LocalHom ** );
  extern int load1SeqWithoutName_new( FILE *fpp, char *cbuf );
  extern char *load1SeqWithoutName_realloc( FILE *fpp );
  extern char *load1SeqWithoutName_realloc_casepreserve( FILE *fpp );
  extern int disttbfast( char **in, int nlen[M], char name[M][B] );
  extern void searchKUorWA( FILE *fp );
  extern void gapireru( char *res, char *ori, char *gt );
  extern int seqlen( char *seq );
  extern void st_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len );
  extern void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len );
  extern void st_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len );
  extern void st_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len );
  extern void getdiaminofreq_x( float *freq, int clus, char **seq, double *eff, int len );
  extern void new_FinalGapCount_zure( float *fgcp, int clus, char **seq, double *eff, int len, char *s, char *e );
  extern void new_FinalGapCount( float *fgcp, int clus, char **seq, double *eff, int len, char *g );
  extern void new_OpeningGapCount( float *ogcp, int clus, char **seq, double *eff, int len, char *g );
  extern void new_OpeningGapCount_zure( float *ogcp, int clus, char **seq, double *eff, int len, char *s, char *e );
  extern void getGapPattern( float *fgcp, int clus, char **seq, double *eff, int len, char *g );
  extern void getgapfreq( float *freq, int clus, char **seq, double *eff, int len );
  extern void getgapfreq_zure( float *freq, int clus, char **seq, double *eff, int len );
  //extern void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *s );
  extern void getgapfreq_zure_part( float *freq, int clus, char **seq, double *eff, int len, char *s );
  extern void getdiaminofreq_part( float *freq, int clus, char **seq, double *eff, int len, char *s, char *e );
  extern void getdigapfreq_part( float *freq, int clus, char **seq, double *eff, int len, char *s, char *e );
  extern void getdiaminofreq_st( float *freq, int clus, char **seq, double *eff, int len );
  extern void getdigapfreq_st( float *freq, int clus, char **seq, double *eff, int len );
  extern void st_getGapPattern( Gappat **gpat, int clus, char **seq, double *eff, int len );
  extern void getkyokaigap( char *g, char **s, int pos, int n );
  extern double *loadaamtx( void );
  extern float naivepairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
  extern float naivepairscore11( char *seq1, char *seq2, int penal );
  extern float naiveQpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
  extern float naiveRpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
  extern float naiveHpairscore( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, int penal );
  extern void foldrna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *pair );
  extern void foldrna_gappick( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, float **impmtx, int *gapmap1, int *gapmap2, RNApair *pair );
  extern void imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
  extern void imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
  extern void part_imp_rnaQ( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
  extern void part_imp_rna( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
  extern void imp_rnaQ_gappick( int nseq1, int nseq2, char **seq1, char **seq2, double *eff1, double *eff2, RNApair ***gr1, RNApair ***gr2, int *gapmap1, int *gapmap2, RNApair *pair );
  extern void foldalignedrna( int clus1, int clus2, char **mseq1, char **mseq2, double *effarr1, double *effarr2, RNApair *rnapairboth );
  void readmccaskill( FILE *fp, RNApair **pairprob, int length );
  void makegrouprna( RNApair ***group, RNApair ***all, int *memlist );
  void makegrouprnait( RNApair ***group, RNApair ***all, char **pair, int s );
  extern void fixed_musclesupg_float_realloc_nobk_halfmtx( int nseq, float **eff, int ***topol, float **len, Treedep * );
  extern void loadtree( int nseq, int ***topol, float **len, char **name, int *nlen, Treedep * );
  extern void loadtop( int nseq, float **eff, int ***topol, float **len );
  extern void fixed_musclesupg_float_realloc_nobk_halfmtx_treeout( int nseq, float **eff, int ***topol, float **len, char **name, int *nlen, Treedep * );
  extern void fixed_musclesupg_double_treeout( int nseq, double **eff, int ***topol, double **len, char **name );
  extern void imp_match_init_strict( float *imp, int clus1, int clus2, int lgth1, int lgth2, char **seq1, char **seq2, double *eff1, double *eff2, double *eff1kozo, double*eff2kozo, LocalHom ***localhom, int forscore );
  extern void miyataout_reorder_pointer( FILE *fp, int locnjob, int nlenmax, char **name, int *nlen, char **aseq, int *order );
  extern void veryfastsupg_double_outtree( int nseq, double **eff, int ***topol, double **len, char **name );
  extern void cpmx_ribosum( char **seq, char **seqr, char *dir, float **cpmx, double *eff, int lgth, int clus );
  extern void rnaalifoldcall( char **seq, int nseq, RNApair **pairprob );
  extern void readpairfoldalign( FILE *fp, char *seq1, char *seq2, char *aln1, char *aln2, int q1, int q2, int *of1, int *of2, int sumlen );
  extern void write1seq( FILE *fp, char *aseq );
  extern void assignstrweight( int nseq, double *strweight, Node *stopol, int ***topol, int step, int LorR, char *kozoari, double *seqweight );
  extern void cutData( FILE *, int **, char **, int * );
  extern void cutAlignment( FILE *, int **, char **, int *, char **, char ** );
  extern void catData( FILE * );
  extern void getnumlen_nogap_outallreg_web( FILE *fp, FILE *ofp, int *nlenminpt, int *isalignedpt );
  extern void getnumlen_nogap_outallreg( FILE *fp, int *nlenminpt );
  extern double plainscore( int nseq, char **seq );
  extern void eq2dash( char *s );
  extern void findnewgaps( int n, char **seq, int *gaplen );
  extern void findcommongaps( int, char **, int * );
  extern void adjustgapmap( int, int *, char * );
  extern void insertnewgaps( int njob, int *alreadyaligned, char **seq, int *ex1, int *ex2, int *gaplen, int *gapmap, int alloclen, char alg );
  extern void restorecommongaps( int n, char **seq, int *top0, int *top1, int *gaplen, int alloclen );
  extern int samemember( int *mem, int *cand );
  extern int includemember( int *mem, int *cand );
  extern void profilealignment( int n0, int n1, int n2, char **aln0, char **aln1, char **aln2, int alloclen, char alg );
  