/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/ |
H A D | dnadist.h | 23 freqar, freqcy, freqgr, freqty, cvi, invarfrac, sumrates, fracchange;
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H A D | dnadist.cpp | 66 freqar, freqcy, freqgr, freqty, cvi, invarfrac, sumrates, fracchange; variable 890 &freqgr, &freqty, &ttratio, &xi, &xv, &fracchange, in getinput() 924 &freqgr, &freqty, &ttratio, &xi, &xv, &fracchange, in getinput() 1156 (xx2[0] * freqar + xx2[(long)G - (long)A] * freqgr) + in makev()
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H A D | protdist.cpp | 519 double aa, bb, freqr, freqy, freqgr, freqty; in transition() local 523 freqgr = freqg / freqr; in transition() 526 bb = freqa * freqgr + freqc * freqty; in transition()
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H A D | DistanceMatrix.cpp | 102 …getbasefreqs(freqa, freqc, freqg, freqt, &freqr, &freqy, &freqar, &freqcy, &freqgr, &freqty, &ttra… in calculateOutOfAlignment()
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H A D | seq.cpp | 380 double *freqgr, double *freqty, double *ttratio, double *xi, in getbasefreqs() argument 402 *freqgr = freqg / *freqr; in getbasefreqs() 406 bb = freqa * (*freqgr) + freqc * (*freqty); in getbasefreqs() 426 *fracchange = (*xi) * (2 * freqa * (*freqgr) + 2 * freqc * (*freqty)) + in getbasefreqs()
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/dports/biology/fluctuate/fluctuate1.4/ |
H A D | getdata.c | 328 dna->freqgr = dna->freqg / dna->freqr; in getbasefreqs() 333 bb = dna->freqa * dna->freqgr + dna->freqc * dna->freqty; in getbasefreqs() 346 dna->fracchange = dna->xi * (2 * dna->freqa * dna->freqgr + in getbasefreqs()
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H A D | fluctuate.h | 284 freqgr, freqty; /* base frequencies */ member
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H A D | fluctuate.c | 1765 sumr1 = dna->freqar * xx1[baseA] + dna->freqgr * xx1[baseG]; in nuview() 1766 sumr2 = dna->freqar * xx2[baseA] + dna->freqgr * xx2[baseG]; in nuview()
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/dports/biology/fastdnaml/fastDNAml_1.2.2/source/ |
H A D | fastDNAml.h | 113 freqar, freqcy, freqgr, freqty; member
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H A D | fastDNAml.c | 1965 rdta->freqgr = rdta->freqg * rdta->invfreqr; in reportfreqs() 1973 sumb = rdta->freqa*rdta->freqgr + rdta->freqc*rdta->freqty; in reportfreqs() 1990 rdta->fracchange = 2.0 * rdta->xi * (rdta->freqa * rdta->freqgr in reportfreqs()
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/dports/biology/migrate/migrate-3.6.11/src/ |
H A D | tree.c | 3085 freqgr = seq->basefrequencies[NUC_GR]; in nuview_sequence() 3204 sumr1 = freqar * xx1t0 + freqgr * xx1t2; in nuview_sequence() 3205 sumr2 = freqar * xx2t0 + freqgr * xx2t2; in nuview_sequence() 3278 freqgr = seq->basefrequencies[NUC_GR]; in nuview_sequence_slow() 3425 sumr1 = freqar * xx1t0 + freqgr * xx1t2; in nuview_sequence_slow() 3426 sumr2 = freqar * xx2t0 + freqgr * xx2t2; in nuview_sequence_slow() 3615 freqgr = seq->basefrequencies[NUC_GR]; in pseudonu_seq() 3669 sumr1 = freqar * xx1t0 + freqgr * xx1t2; in pseudonu_seq() 3819 freqgr = seq->basefrequencies[NUC_GR]; in pseudonu_seq_slow() 3967 sumr1 = freqar * xx1t0 + freqgr * xx1t2; in pseudonu_seq_slow() [all …]
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H A D | sequence.c | 408 register MYREAL /*freqar, freqcy,*/ freqgr, freqty; in getbasefreqs() local 447 freqgr = seq->basefrequencies[NUC_GR]; in getbasefreqs() 453 bb = freqa * (freqgr) + freqc * (freqty); in getbasefreqs() 472 (seq->xi) * (2. * freqa * (freqgr) + in getbasefreqs()
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H A D | migration.h | 194 MYREAL freqar, freqcy, freqgr, freqty; //!< frequency of transitions member
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/dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
H A D | dlmodel.cpp | 670 freqgr(FLAGDOUBLE), freqty(FLAGDOUBLE), in F84Model() 763 freqgr = src.freqgr; in CopyMembers() 856 freqgr = freqg / pur; in Finalize() 870 double fracchange = y * (2.0 * freqa * freqgr + 2.0 * freqc * freqty) in Finalize() 1047 sumPur = freqar*catDLs1[baseA] + freqgr*catDLs1[baseG]; in ComputeSiteDLs() 1098 sumPur = freqar*catDLs2[baseA] + freqgr*catDLs2[baseG]; in ComputeSiteDLs()
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H A D | dlmodel.h | 240 double freqar, freqcy, freqgr, freqty; variable
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/dports/biology/recombine/recombine1.41/ |
H A D | getdata.c | 1199 dna->freqgr = dna->freqg / dna->freqr; in getbasednafreqs() 1204 bb = dna->freqa * dna->freqgr + dna->freqc * dna->freqty; in getbasednafreqs() 1217 dna->fracchange = dna->xi * (2 * dna->freqa * dna->freqgr + in getbasednafreqs()
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H A D | recombine.h | 386 freqgr, freqty; /* base frequencies */ member
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H A D | recombine.c | 4098 sumr1 = dna->freqar * xx1[k][baseA] + dna->freqgr * xx1[k][baseG]; in calcrange() 4128 sumr2 = dna->freqar * xx2[k][baseA] + dna->freqgr * xx2[k][baseG]; in calcrange()
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/dports/biology/seaview/seaview/csrc/ |
H A D | seq.c | 374 double *freqgr, double *freqty, double *ttratio, double *xi, in getbasefreqs() argument 396 *freqgr = freqg / *freqr; in getbasefreqs() 399 bb = freqa * (*freqgr) + freqc * (*freqty); in getbasefreqs() 419 *fracchange = (*xi) * (2 * freqa * (*freqgr) + 2 * freqc * (*freqty)) + in getbasefreqs()
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