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Searched refs:branchLengths (Results 1 – 22 of 22) sorted by relevance

/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/
H A DAnalyzeCodonData.bf23 ChoiceList (branchLengths, "Branch Lengths", 1, SKIP_NONE,
27 if (branchLengths < 0)
32 if (branchLengths == 1)
H A DBivariateCodonRateAnalysis.bf17 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE,
22 assert (branchLengths >= 0);
32 if (branchLengths == 0)
H A DAAModelComparison.bf82 branchLengths = BranchLength (givenTree,-1);
84 for (k=Rows(branchLengths)*Columns(branchLengths)-1; k>=0; k=k-1)
86 TL = TL + branchLengths[k];
H A DdNdSBivariateRateAnalysis.bf68 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE,
73 if (branchLengths<0)
563 if (branchLengths)
619 GetInformation (branchLengths, "^codonFactor$");
621 //Sfprintf (stdout, "\n\n",branchLengths,"\n\n");
623 branchLengths = (Columns (branchLengths)>0);
720 … - branchLengths; /* remove one more for codon scaling factor, if nuc branch lengths are used */
H A DSGASimProcessor.bf131 branchLengths = BranchLength(givenTree,-1);
133 for (v=Columns(branchLengths)-1; v>=0; v=v-1)
135 totalTreeLength = totalTreeLength + branchLengths[v];
214 branchFactor = branchLengths[p1]/totalTreeLength;
241 branchFactor = branchLengths[p1]/totalTreeLength;
H A DdNdSRateAnalysis.bf227 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE,
236 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE,
242 if (branchLengths<0)
249 if (branchLengths<2)
263 if (branchLengths == 2)
593 doNucFit = (branchLengths<2);
627 if (branchLengths == 1)
634 if (branchLengths == 0)
820 if (branchLengths)
H A DSGIvL.bf213 branchLengths = BranchLength(givenTree,-1);
217 for (v=Columns(branchLengths)-1; v>=0; v=v-1)
219 totalTreeLength = totalTreeLength + branchLengths[v];
223 internalBL = internalBL + branchLengths[v];
308 branchFactor = branchLengths[p1]/internalBL;
338 branchFactor = branchLengths[p1]/terminalBL;
H A DMGvsGY.bf474 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE,
479 if (branchLengths<0)
541 if (branchLengths)
561 if (branchLengths)
579 if (branchLengths)
H A DdNdSDistributionComparison.bf230 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE,
235 if (branchLengths<0)
432 if (branchLengths)
738 degF = Columns(paramList["Global Independent"]) + 14 - 2*branchLengths + treeBranchParameters;
782 degFPSS = Columns(paramList["Global Independent"]) + 14 - 2*branchLengths + treeBranchParameters;
829 degFPSP = Columns(paramList["Global Independent"]) + 14 - 2*branchLengths + treeBranchParameters;
882 degFPSH = Columns(paramList["Global Independent"]) + 14 - 2*branchLengths + treeBranchParameters;
937 degFJ = Columns(paramList["Global Independent"]) + 14 - 2*branchLengths + treeBranchParameters;
H A DSGEmulator_MF.bf223 ExecuteCommands ("branchLengths = BranchLength(nucTree_"+fileID+",-1);");
224 for (v=Columns(branchLengths)-1; v>=0; v=v-1)
226 totalTreeLength = totalTreeLength + branchLengths[v];
307 branchFactor = branchLengths[p1]/totalTreeLength;
343 branchFactor = branchLengths[p1]/totalTreeLength;
H A DSGEmulator.bf334 branchLengths = BranchLength(givenTree,-1);
336 for (v=Columns(branchLengths)-1; v>=0; v=v-1)
338 totalTreeLength = totalTreeLength + branchLengths[v];
409 …anchNamesList[v]+".synRate = codonTree."+branchNamesList[v]+".synRate*branchLengths[v]/branchLengt…
461 branchFactor = branchLengths[p1]/totalTreeLength;
496 branchFactor = branchLengths[p1]/totalTreeLength;
H A DNucModelCompare.bf478 branchLengths = 0;
482 ChoiceList (branchLengths,"Estimate Branch Lengths",1,SKIP_NONE,
487 if (branchLengths<0)
586 if (branchLengths > 0)
616 if (branchLengths)
735 if (branchLengths)
H A DTestClade.bf295 function ModelSelect (modelType, branchLengths, rejectAt)
364 if (branchLengths == 0)
373 if (branchLengths)
391 if (branchLengths)
510 if (branchLengths)
H A DPARRIS.bf228 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE,
233 if (branchLengths<0)
540 if (branchLengths)
542 branchLengths = -branchLengths;
695 if (branchLengths)
835 if (branchLengths)
H A DCodonModelCompare.bf616 ChoiceList (branchLengths,"Estimate Branch Lengths",1,SKIP_NONE,
621 if (branchLengths<0)
666 if (branchLengths)
/dports/biology/hyphy/hyphy-2.5.33/src/core/
H A Dtopology.cpp1156 hyFloat myLength = branchLengths.get_direct(myIndex); in FindCOTHelper()
1180 hyFloat myLength = myIndex>=0?branchLengths.theData [myIndex]:0.0; in FindCOTHelper2()
1485 branchLengths (1, branchCount+leafCount, false, true), in FindCOT() local
1501 branchLengths.Store (0, tIndex++, myLength); in FindCOT()
1515 myLength = branchLengths.theData[childIndex]; in FindCOT()
1542 hyFloat myLength = branchLengths.theData[childIndex]; in FindCOT()
1571 hyFloat T = branchLengths.theData[ci]; in FindCOT()
1656 resList->MStore (kCOTBranchLength, new _Constant (branchLengths.directIndex(tIndex)), false); in FindCOT()
1660 …indCOTHelper2 (cotBranch, branchSpans, branchLengths, addressToIndexMap2, nil, currentBranchSplit… in FindCOT()
1662 hyFloat adjuster = branchLengths.theData [tIndex]-currentBranchSplit; in FindCOT()
[all …]
/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/UnitTests/HBLCommands/
H A DFormat.bf42 …// Format a Topology in an easy to read string (topology, internalNodeNames*, branchLengths*) *: i…
/dports/biology/mrbayes/MrBayes-3.2.7/src/
H A Dmbbeagle.c86 m->branchLengths = (MrBFlt *) SafeCalloc (2*numLocalTaxa, sizeof(MrBFlt)); in InitBeagleInstance()
1454 m->branchLengths[count] = length; in TreeTiProbs_Beagle()
1459 printf("%d %f ", count, m->branchLengths[count]); in TreeTiProbs_Beagle()
1478 m->branchLengths, in TreeTiProbs_Beagle()
1561 m->branchLengths = (MrBFlt *) SafeCalloc (sizePD*2*numLocalTaxa, sizeof(MrBFlt)); in InitBeagleMultiPartitionInstance()
2003 branchLengthsAll = modelSettings[0].branchLengths; in TreeTiProbs_BeagleMultiPartition()
H A Dbayes.h1376 MrBFlt* branchLengths; /* array of branch lengths for Beagle */ member
H A Dmcmc.c4671 SAFEFREE(m->branchLengths); in FreeChainMemory()
H A Dmodel.c17825 m->branchLengths = NULL; /* array of branch lengths for Beagle */ in SetModelInfo()
/dports/textproc/gitlab-elasticsearch-indexer/gitlab-elasticsearch-indexer-ef1440548effec15831eda2d246dacc43233cefb/vendor/github.com/go-enry/go-enry/v2/internal/code-generator/generator/test_files/
H A Dfrequencies.gold53314 "branchLengths": -7.648740,