/dports/biology/hyphy/hyphy-2.5.33/res/TemplateBatchFiles/ |
H A D | AnalyzeCodonData.bf | 23 ChoiceList (branchLengths, "Branch Lengths", 1, SKIP_NONE, 27 if (branchLengths < 0) 32 if (branchLengths == 1)
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H A D | BivariateCodonRateAnalysis.bf | 17 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE, 22 assert (branchLengths >= 0); 32 if (branchLengths == 0)
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H A D | AAModelComparison.bf | 82 branchLengths = BranchLength (givenTree,-1); 84 for (k=Rows(branchLengths)*Columns(branchLengths)-1; k>=0; k=k-1) 86 TL = TL + branchLengths[k];
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H A D | dNdSBivariateRateAnalysis.bf | 68 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 */
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H A D | SGASimProcessor.bf | 131 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;
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H A D | dNdSRateAnalysis.bf | 227 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)
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H A D | SGIvL.bf | 213 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;
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H A D | MGvsGY.bf | 474 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE, 479 if (branchLengths<0) 541 if (branchLengths) 561 if (branchLengths) 579 if (branchLengths)
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H A D | dNdSDistributionComparison.bf | 230 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;
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H A D | SGEmulator_MF.bf | 223 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;
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H A D | SGEmulator.bf | 334 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;
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H A D | NucModelCompare.bf | 478 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)
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H A D | TestClade.bf | 295 function ModelSelect (modelType, branchLengths, rejectAt) 364 if (branchLengths == 0) 373 if (branchLengths) 391 if (branchLengths) 510 if (branchLengths)
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H A D | PARRIS.bf | 228 ChoiceList (branchLengths,"Branch Lengths",1,SKIP_NONE, 233 if (branchLengths<0) 540 if (branchLengths) 542 branchLengths = -branchLengths; 695 if (branchLengths) 835 if (branchLengths)
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H A D | CodonModelCompare.bf | 616 ChoiceList (branchLengths,"Estimate Branch Lengths",1,SKIP_NONE, 621 if (branchLengths<0) 666 if (branchLengths)
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/dports/biology/hyphy/hyphy-2.5.33/src/core/ |
H A D | topology.cpp | 1156 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 …]
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/dports/biology/hyphy/hyphy-2.5.33/tests/hbltests/UnitTests/HBLCommands/ |
H A D | Format.bf | 42 …// Format a Topology in an easy to read string (topology, internalNodeNames*, branchLengths*) *: i…
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/dports/biology/mrbayes/MrBayes-3.2.7/src/ |
H A D | mbbeagle.c | 86 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()
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H A D | bayes.h | 1376 MrBFlt* branchLengths; /* array of branch lengths for Beagle */ member
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H A D | mcmc.c | 4671 SAFEFREE(m->branchLengths); in FreeChainMemory()
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H A D | model.c | 17825 m->branchLengths = NULL; /* array of branch lengths for Beagle */ in SetModelInfo()
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/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 D | frequencies.gold | 53314 "branchLengths": -7.648740,
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