Home
last modified time | relevance | path

Searched refs:freqgr (Results 1 – 19 of 19) sorted by relevance

/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/
H A Ddnadist.h23 freqar, freqcy, freqgr, freqty, cvi, invarfrac, sumrates, fracchange;
H A Ddnadist.cpp66 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()
H A Dprotdist.cpp519 double aa, bb, freqr, freqy, freqgr, freqty; in transition() local
523 freqgr = freqg / freqr; in transition()
526 bb = freqa * freqgr + freqc * freqty; in transition()
H A DDistanceMatrix.cpp102 …getbasefreqs(freqa, freqc, freqg, freqt, &freqr, &freqy, &freqar, &freqcy, &freqgr, &freqty, &ttra… in calculateOutOfAlignment()
H A Dseq.cpp380 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()
/dports/biology/fluctuate/fluctuate1.4/
H A Dgetdata.c328 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()
H A Dfluctuate.h284 freqgr, freqty; /* base frequencies */ member
H A Dfluctuate.c1765 sumr1 = dna->freqar * xx1[baseA] + dna->freqgr * xx1[baseG]; in nuview()
1766 sumr2 = dna->freqar * xx2[baseA] + dna->freqgr * xx2[baseG]; in nuview()
/dports/biology/fastdnaml/fastDNAml_1.2.2/source/
H A DfastDNAml.h113 freqar, freqcy, freqgr, freqty; member
H A DfastDNAml.c1965 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()
/dports/biology/migrate/migrate-3.6.11/src/
H A Dtree.c3085 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 …]
H A Dsequence.c408 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()
H A Dmigration.h194 MYREAL freqar, freqcy, freqgr, freqty; //!< frequency of transitions member
/dports/biology/lamarc/lamarc-2.1.8/src/datalike/
H A Ddlmodel.cpp670 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()
H A Ddlmodel.h240 double freqar, freqcy, freqgr, freqty; variable
/dports/biology/recombine/recombine1.41/
H A Dgetdata.c1199 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()
H A Drecombine.h386 freqgr, freqty; /* base frequencies */ member
H A Drecombine.c4098 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()
/dports/biology/seaview/seaview/csrc/
H A Dseq.c374 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()