| /dports/biology/mafft/mafft-7.267-without-extensions/core/ |
| H A D | MSalign11.c | 8 static void extendmseq( char **mseq1, char **mseq2, char **seq1, char **seq2, int i, int j, int pre… in extendmseq()
49 char **mseq1, char **mseq2, in Atracking()
121 …icalw, double *m, int *mp, int iin, int jin, char **seq1, char **seq2, char **mseq1, char **mseq2 ) in backdp()
315 static char **mseq1; in MSalign11() local
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| H A D | getlag.c | 157 void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, doubl… in treebase()
330 static char **mseq1, **mseq2; in main() local
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| H A D | mafft-profile.c | 179 …nt nseq1, int nseq2, char **name, int *nlen, char **seq, char **aseq, char **mseq1, char **mseq2, … in GroupAlign()
312 static char **mseq1, **mseq2; in main() local
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| H A D | SAalignmm.c | 51 char **mseq1, char **mseq2, in Atracking()
177 static TLS char **mseq1; in Aalign() local
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| H A D | pairash.c | 332 static double calltmalign( char **mseq1, char **mseq2, double *equiv, char *fname1, char *chain1, c… in calltmalign()
409 static double callrash( int mem1, int mem2, char **mseq1, char **mseq2, double *equiv, char *fname1… in callrash()
1024 static void pairalign( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq… in pairalign()
1318 static char **mseq1, **mseq2; in main() local
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| H A D | rnatest.c | 329 static char **mseq1, **mseq2; in main() local
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| H A D | pairlocalalign.c | 236 static double recallpairfoldalign( char **mseq1, char **mseq2, int m1, int m2, int *of1pt, int *of2… in recallpairfoldalign()
1214 static double recalllara( char **mseq1, char **mseq2, int alloclen ) in recalllara()
1277 static double calldafs_giving_bpp( char **mseq1, char **mseq2, char **bpp1, char **bpp2, int allocl… in calldafs_giving_bpp()
1394 static double callmxscarna_giving_bpp( char **mseq1, char **mseq2, char **bpp1, char **bpp2, int al… in callmxscarna_giving_bpp()
1939 char **mseq1, **mseq2, **distseq1, **distseq2, **dumseq1, **dumseq2; in athread() local
2329 … *nlen, char **seq, char **aseq, char **dseq, int *thereisxineachseq, char **mseq1, char **mseq2, … in pairalign()
2926 char **mseq1, **mseq2; in main() local
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| H A D | MSalignmm.c | 176 char **mseq1, char **mseq2, in Atracking()
323 … int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, … in MSalignmm_tanni()
635 … int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, … in MSalignmm_rec()
1654 char **mseq1, in freearrays()
1680 char **mseq1; in MSalignmm() local
1928 … int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, … in MSalignmm_tanni_variousdist()
2243 … int ien, int jst, int jen, int alloclen, int fulllen1, int fulllen2, char **mseq1, char **mseq2, … in MSalignmm_rec_variousdist()
3293 char **mseq1, in freearrays_variousdist()
3321 char **mseq1; in MSalignmm_variousdist() local
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| H A D | genalign11.c | 32 char **mseq1, char **mseq2, in gentracking()
141 static TLS char **mseq1; in genL__align11() local
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| H A D | Lalignmm.c | 346 …x1, double **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, … in MSalign2m2m_rec()
1246 …x1, double **cpmx2, int ist, int ien, int jst, int jen, int alloclen, char **mseq1, char **mseq2, … in MSalignmm_rec()
2168 char **mseq1; in Lalignmm_hmout() local
2371 char **mseq1; in Lalign2m2m_hmout() local
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| H A D | suboptalign11.c | 40 char **mseq1, char **mseq2, in gentracking()
158 static char **mseq1; in suboptalign11() local
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| H A D | iteration.c | 103 static char *mseq1, **mseq2 = NULL; in iteration() local
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| H A D | Galign11.c | 29 char **mseq1, char **mseq2, in Atracking()
198 static TLS char **mseq1 = NULL; in G__align11() local
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| H A D | Lalign11.c | 93 char **mseq1, char **mseq2, in Ltracking()
232 static TLS char **mseq1; in L__align11() local
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| H A D | tbfast.c | 540 char **mseq1, **mseq2; in treebasethread() local
915 void treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, in… in treebase()
1372 static char **mseq1, **mseq2; in main() local
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| H A D | Salignmm.c | 743 char **mseq1, char **mseq2, in Atracking_localhom()
882 char **mseq1, char **mseq2, in Atracking()
1043 static TLS char **mseq1; in A__align() local
1810 static TLS char **mseq1; in A__align_variousdist() local
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| H A D | partSalignmm.c | 669 char **mseq1, char **mseq2, in Atracking_localhom()
817 char **mseq1, char **mseq2, in Atracking()
981 static TLS char **mseq1; in partA__align() local
1669 static TLS char **mseq1; in partA__align_variousdist() local
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| H A D | tditeration.c | 256 char **mseq1, char **mseq2, in freelocalarrays()
369 char **mseq1, **mseq2; in athread() local
1267 static char **mseq1, **mseq2; local
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| H A D | disttbfast.c | 903 char **mseq1, **mseq2; in treebasethread() local
1299 static int treebase( int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mse… in treebase() argument
1836 char **mseq1 = NULL, **mseq2 = NULL; in disttbfast() local
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| H A D | makedirectionlist.c | 334 char **mseq1, **mseq2; in directionthread() local
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| H A D | mltaln9.c | 197 char *mseq1, *mseq2; in intergroup_score_consweight() local
262 char *mseq1, *mseq2; in intergroup_score_gapnomi() local
328 char *mseq1, *mseq2; in intergroup_score_multimtx() local
406 char *mseq1, *mseq2; in intergroup_score_dynmtx() local
482 char *mseq1, *mseq2; in intergroup_score() local
556 char *mseq1, *mseq2; in intergroup_score_new() local
619 char *mseq1, *mseq2; in score_calc5() local
740 char *mseq1, *mseq2; in score_calc4() local
5798 void FreeTmpSeqs( char **mseq2, char *mseq1 ) in FreeTmpSeqs()
6174 char *mseq1, *mseq2; in score_calc_for_score() local
[all …]
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| H A D | addfunctions.c | 451 char **mseq2, **mseq0, **mseq1; in insertnewgaps() local
682 char **mseq2, **mseq0, **mseq1; in insertnewgaps_bothorders() local
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| H A D | splittbfast.c | 937 static char **mseq1, **mseq2; in pairalign() local
1200 static char **mseq1 = NULL; in splitseq_mq() local
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| H A D | Dalignmm.c | 635 char **mseq1, char **mseq2, in Atracking_localhom()
774 char **mseq1, char **mseq2, in Atracking()
2737 static TLS char **mseq1; in D__align() local
4573 static TLS char **mseq1; in D__align_variousdist() local
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| H A D | addsingle.c | 1150 …base( int nseq, int *nlen, char **aseq, int nadd, char *mergeoralign, char **mseq1, char **mseq2, … in treebase()
1549 char **mseq1 = NULL, **mseq2 = NULL; in addsinglethread() local
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