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/fastml-3.11/libs/phylogeny/bestHKYparam.h
Examining data/fastml-3.11/libs/phylogeny/hky.h
Examining data/fastml-3.11/libs/phylogeny/computePosteriorExpectationOfSubstitutions.h
Examining data/fastml-3.11/libs/phylogeny/computePosteriorExpectationOfSubstitutions_nonReversibleSp.h
Examining data/fastml-3.11/libs/phylogeny/betaDistributionFixedCategoriesWithOmegaUniform.cpp
Examining data/fastml-3.11/libs/phylogeny/nj.cpp
Examining data/fastml-3.11/libs/phylogeny/bestAlpha.h
Examining data/fastml-3.11/libs/phylogeny/splitTreeUtil.cpp
Examining data/fastml-3.11/libs/phylogeny/fromInstructionFile.h
Examining data/fastml-3.11/libs/phylogeny/fastaFormat.h
Examining data/fastml-3.11/libs/phylogeny/simulateRateShiftJumps.cpp
Examining data/fastml-3.11/libs/phylogeny/phylipSequentialFormat.h
Examining data/fastml-3.11/libs/phylogeny/gammaDistributionLaguerre.h
Examining data/fastml-3.11/libs/phylogeny/codonJC.cpp
Examining data/fastml-3.11/libs/phylogeny/likeDistPropEB.cpp
Examining data/fastml-3.11/libs/phylogeny/computeMarginalAlg.h
Examining data/fastml-3.11/libs/phylogeny/countTableComponent.cpp
Examining data/fastml-3.11/libs/phylogeny/fromCountTableComponentToDistanceProp.cpp
Examining data/fastml-3.11/libs/phylogeny/simulateJumpsAbstract.cpp
Examining data/fastml-3.11/libs/phylogeny/betaOmegaDistribution.h
Examining data/fastml-3.11/libs/phylogeny/AddLog.cpp
Examining data/fastml-3.11/libs/phylogeny/checkcovFanctors.h
Examining data/fastml-3.11/libs/phylogeny/hky.cpp
Examining data/fastml-3.11/libs/phylogeny/treeIt.cpp
Examining data/fastml-3.11/libs/phylogeny/integerAlphabet.cpp
Examining data/fastml-3.11/libs/phylogeny/aaJC.cpp
Examining data/fastml-3.11/libs/phylogeny/datMatrixHolder.h
Examining data/fastml-3.11/libs/phylogeny/betaDistributionFixedCategories.cpp
Examining data/fastml-3.11/libs/phylogeny/posteriorDistance.cpp
Examining data/fastml-3.11/libs/phylogeny/pairwiseGammaDistance.cpp
Examining data/fastml-3.11/libs/phylogeny/bestAlpha.cpp
Examining data/fastml-3.11/libs/phylogeny/bestGtrModelParams.h
Examining data/fastml-3.11/libs/phylogeny/bblEMProportionalEB.h
Examining data/fastml-3.11/libs/phylogeny/bestTamura92param.h
Examining data/fastml-3.11/libs/phylogeny/simulateTree.h
Examining data/fastml-3.11/libs/phylogeny/optGammaMixtureEM.h
Examining data/fastml-3.11/libs/phylogeny/computeMarginalAlg.cpp
Examining data/fastml-3.11/libs/phylogeny/multipleStochasticProcess.cpp
Examining data/fastml-3.11/libs/phylogeny/indelModel.h
Examining data/fastml-3.11/libs/phylogeny/bootstrap.h
Examining data/fastml-3.11/libs/phylogeny/optGammaMixtureLS.cpp
Examining data/fastml-3.11/libs/phylogeny/bestParamUSSRV.h
Examining data/fastml-3.11/libs/phylogeny/talRandom.h
Examining data/fastml-3.11/libs/phylogeny/GamMixtureOptimizer.h
Examining data/fastml-3.11/libs/phylogeny/simulateWithDependence.cpp
Examining data/fastml-3.11/libs/phylogeny/bblEM2codon.h
Examining data/fastml-3.11/libs/phylogeny/datMatrixHolder.cpp
Examining data/fastml-3.11/libs/phylogeny/bblEMfixRoot.cpp
Examining data/fastml-3.11/libs/phylogeny/AddLog.h
Examining data/fastml-3.11/libs/phylogeny/errorMsg.cpp
Examining data/fastml-3.11/libs/phylogeny/NNiSep.h
Examining data/fastml-3.11/libs/phylogeny/someUtil.cpp