Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/rate4site-3.0.0/src/phylogeny/getopt.h
Examining data/rate4site-3.0.0/src/phylogeny/errorMsg.h
Examining data/rate4site-3.0.0/src/phylogeny/definitions.h
Examining data/rate4site-3.0.0/src/phylogeny/doubleRep.h
Examining data/rate4site-3.0.0/src/phylogeny/ConversionUtils.h
Examining data/rate4site-3.0.0/src/phylogeny/sequenceContainer.h
Examining data/rate4site-3.0.0/src/phylogeny/sequence.h
Examining data/rate4site-3.0.0/src/phylogeny/alphabet.h
Examining data/rate4site-3.0.0/src/phylogeny/mulAlphabet.h
Examining data/rate4site-3.0.0/src/phylogeny/someUtil.h
Examining data/rate4site-3.0.0/src/phylogeny/logFile.h
Examining data/rate4site-3.0.0/src/phylogeny/gainLossAlphabet.h
Examining data/rate4site-3.0.0/src/phylogeny/pijAccelerator.h
Examining data/rate4site-3.0.0/src/phylogeny/replacementModel.h
Examining data/rate4site-3.0.0/src/phylogeny/distribution.h
Examining data/rate4site-3.0.0/src/phylogeny/readTree.h
Examining data/rate4site-3.0.0/src/phylogeny/nucleotide.h
Examining data/rate4site-3.0.0/src/phylogeny/amino.h
Examining data/rate4site-3.0.0/src/phylogeny/geneticCodeHolder.h
Examining data/rate4site-3.0.0/src/phylogeny/codon.h
Examining data/rate4site-3.0.0/src/phylogeny/evaluateCharacterFreq.h
Examining data/rate4site-3.0.0/src/phylogeny/uniDistribution.h
Examining data/rate4site-3.0.0/src/phylogeny/generalGammaDistribution.h
Examining data/rate4site-3.0.0/src/phylogeny/readDatMatrix.h
Examining data/rate4site-3.0.0/src/phylogeny/datMatrixHolder.h
Examining data/rate4site-3.0.0/src/phylogeny/chebyshevAccelerator.h
Examining data/rate4site-3.0.0/src/phylogeny/nucJC.h
Examining data/rate4site-3.0.0/src/phylogeny/aaJC.h
Examining data/rate4site-3.0.0/src/phylogeny/gtrModel.h
Examining data/rate4site-3.0.0/src/phylogeny/fromQtoPt.h
Examining data/rate4site-3.0.0/src/phylogeny/trivialAccelerator.h
Examining data/rate4site-3.0.0/src/phylogeny/distanceMethod.h
Examining data/rate4site-3.0.0/src/phylogeny/distanceTable.h
Examining data/rate4site-3.0.0/src/phylogeny/nj.h
Examining data/rate4site-3.0.0/src/phylogeny/njConstrain.h
Examining data/rate4site-3.0.0/src/phylogeny/distances2Tree.h
Examining data/rate4site-3.0.0/src/phylogeny/numRec.h
Examining data/rate4site-3.0.0/src/phylogeny/uniformDistribution.h
Examining data/rate4site-3.0.0/src/phylogeny/checkcovFanctors.h
Examining data/rate4site-3.0.0/src/phylogeny/likelihoodComputation.h
Examining data/rate4site-3.0.0/src/phylogeny/computePijComponent.h
Examining data/rate4site-3.0.0/src/phylogeny/stochasticProcess.h
Examining data/rate4site-3.0.0/src/phylogeny/suffStatComponent.h
Examining data/rate4site-3.0.0/src/phylogeny/unObservableData.h
Examining data/rate4site-3.0.0/src/phylogeny/likeDist.h
Examining data/rate4site-3.0.0/src/phylogeny/countTableComponent.h
Examining data/rate4site-3.0.0/src/phylogeny/jcDistance.h
Examining data/rate4site-3.0.0/src/phylogeny/fastStartTree.h
Examining data/rate4site-3.0.0/src/phylogeny/checkcovFanctorsWithFactors.h
Examining data/rate4site-3.0.0/src/phylogeny/likelihoodComputationFactors.h
Examining data/rate4site-3.0.0/src/phylogeny/bestAlpha.h
Examining data/rate4site-3.0.0/src/phylogeny/gammaDistribution.h
Examining data/rate4site-3.0.0/src/phylogeny/siteSpecificRate.h
Examining data/rate4site-3.0.0/src/phylogeny/recognizeFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/bblEM.h
Examining data/rate4site-3.0.0/src/phylogeny/bestGtrModelParams.h
Examining data/rate4site-3.0.0/src/phylogeny/tamura92.h
Examining data/rate4site-3.0.0/src/phylogeny/bestHKYparam.h
Examining data/rate4site-3.0.0/src/phylogeny/hky.h
Examining data/rate4site-3.0.0/src/phylogeny/bestTamura92param.h
Examining data/rate4site-3.0.0/src/phylogeny/talRandom.h
Examining data/rate4site-3.0.0/src/phylogeny/computeSubstitutionCounts.h
Examining data/rate4site-3.0.0/src/phylogeny/fromCountTableComponentToDistance.h
Examining data/rate4site-3.0.0/src/phylogeny/computeCounts.h
Examining data/rate4site-3.0.0/src/phylogeny/computeDownAlg.h
Examining data/rate4site-3.0.0/src/phylogeny/computeUpAlg.h
Examining data/rate4site-3.0.0/src/phylogeny/gammaUtilities.h
Examining data/rate4site-3.0.0/src/phylogeny/seqContainerTreeMap.h
Examining data/rate4site-3.0.0/src/phylogeny/treeUtil.h
Examining data/rate4site-3.0.0/src/phylogeny/matrixUtils.h
Examining data/rate4site-3.0.0/src/phylogeny/computePosteriorExpectationOfSubstitutions.h
Examining data/rate4site-3.0.0/src/phylogeny/computePosteriorExpectationOfSubstitutions_nonReversibleSp.h
Examining data/rate4site-3.0.0/src/phylogeny/multipleStochasticProcess.h
Examining data/rate4site-3.0.0/src/phylogeny/simulateJumps.h
Examining data/rate4site-3.0.0/src/phylogeny/simulateJumpsAbstract.h
Examining data/rate4site-3.0.0/src/phylogeny/simulateCodonsJumps.h
Examining data/rate4site-3.0.0/src/phylogeny/treeIt.h
Examining data/rate4site-3.0.0/src/phylogeny/likelihoodComputationGL.h
Examining data/rate4site-3.0.0/src/phylogeny/tree.h
Examining data/rate4site-3.0.0/src/phylogeny/bblEMProportionalEB.h
Examining data/rate4site-3.0.0/src/phylogeny/fromCountTableComponentToDistancePropEB.h
Examining data/rate4site-3.0.0/src/phylogeny/likeDistPropEB.h
Examining data/rate4site-3.0.0/src/phylogeny/bblLSProportionalEB.h
Examining data/rate4site-3.0.0/src/phylogeny/phylipFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/maseFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/clustalFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/fastaFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/phylipSequentialFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/molphyFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/getRandomWeights.h
Examining data/rate4site-3.0.0/src/phylogeny/nexusFormat.h
Examining data/rate4site-3.0.0/src/phylogeny/alphabet.cpp
Examining data/rate4site-3.0.0/src/phylogeny/sequenceContainer.cpp
Examining data/rate4site-3.0.0/src/phylogeny/sequence.cpp
Examining data/rate4site-3.0.0/src/phylogeny/mulAlphabet.cpp
Examining data/rate4site-3.0.0/src/phylogeny/someUtil.cpp