rate4site - i386

unassigned

rate4siteOptions.cpp

Class

./rate4siteOptions.cpp.002t.class

Gimple

./rate4siteOptions.cpp.004t.gimple

GKD

./rate4siteOptions.o.gkd

OBJ

obj: ./rate4siteOptions.o

unassigned

rate4site.cpp

Class

./rate4site.cpp.002t.class

Gimple

./rate4site.cpp.004t.gimple

GKD

./rate4site.o.gkd

OBJ

obj: ./rate4site.o

unassigned

sequenceContainer.cpp

Class

./sequenceContainer.cpp.002t.class

Gimple

./sequenceContainer.cpp.004t.gimple

GKD

./sequenceContainer.o.gkd

OBJ

obj: ./sequenceContainer.o

unassigned

sequence.cpp

Class

./sequence.cpp.002t.class

Gimple

./sequence.cpp.004t.gimple

GKD

./sequence.o.gkd

OBJ

obj: ./sequence.o

unassigned

mulAlphabet.cpp

Class

./mulAlphabet.cpp.002t.class

Gimple

./mulAlphabet.cpp.004t.gimple

GKD

./mulAlphabet.o.gkd

OBJ

obj: ./mulAlphabet.o

unassigned

someUtil.cpp

Class

./someUtil.cpp.002t.class

Gimple

./someUtil.cpp.004t.gimple

GKD

./someUtil.o.gkd

OBJ

obj: ./someUtil.o

unassigned

logFile.cpp

Class

./logFile.cpp.002t.class

Gimple

./logFile.cpp.004t.gimple

GKD

./logFile.o.gkd

OBJ

obj: ./logFile.o

pijAccelerator.cpp

Class

./pijAccelerator.cpp.002t.class

Gimple

./pijAccelerator.cpp.004t.gimple

GKD

./pijAccelerator.o.gkd

OBJ

obj: ./pijAccelerator.o

replacementModel.cpp

Class

./replacementModel.cpp.002t.class

Gimple

./replacementModel.cpp.004t.gimple

GKD

./replacementModel.o.gkd

OBJ

obj: ./replacementModel.o

distribution.cpp

Class

./distribution.cpp.002t.class

Gimple

./distribution.cpp.004t.gimple

GKD

./distribution.o.gkd

OBJ

obj: ./distribution.o

unassigned

errorMsg.cpp

Class

./errorMsg.cpp.002t.class

Gimple

./errorMsg.cpp.004t.gimple

GKD

./errorMsg.o.gkd

OBJ

obj: ./errorMsg.o

unassigned

nucleotide.cpp

Class

./nucleotide.cpp.002t.class

Gimple

./nucleotide.cpp.004t.gimple

GKD

./nucleotide.o.gkd

OBJ

obj: ./nucleotide.o

unassigned

amino.cpp

Class

./amino.cpp.002t.class

Gimple

./amino.cpp.004t.gimple

GKD

./amino.o.gkd

OBJ

obj: ./amino.o

unassigned

evaluateCharacterFreq.cpp

Class

./evaluateCharacterFreq.cpp.002t.class

Gimple

./evaluateCharacterFreq.cpp.004t.gimple

GKD

./evaluateCharacterFreq.o.gkd

OBJ

obj: ./evaluateCharacterFreq.o

unassigned

uniDistribution.cpp

Class

./uniDistribution.cpp.002t.class

Gimple

./uniDistribution.cpp.004t.gimple

GKD

./uniDistribution.o.gkd

OBJ

obj: ./uniDistribution.o

unassigned

generalGammaDistribution.cpp

Class

./generalGammaDistribution.cpp.002t.class

Gimple

./generalGammaDistribution.cpp.004t.gimple

GKD

./generalGammaDistribution.o.gkd

OBJ

obj: ./generalGammaDistribution.o

unassigned

readDatMatrix.cpp

Class

./readDatMatrix.cpp.002t.class

Gimple

./readDatMatrix.cpp.004t.gimple

GKD

./readDatMatrix.o.gkd

OBJ

obj: ./readDatMatrix.o

unassigned

datMatrixHolder.cpp

Class

./datMatrixHolder.cpp.002t.class

Gimple

./datMatrixHolder.cpp.004t.gimple

GKD

./datMatrixHolder.o.gkd

OBJ

obj: ./datMatrixHolder.o

unassigned

chebyshevAccelerator.cpp

Class

./chebyshevAccelerator.cpp.002t.class

Gimple

./chebyshevAccelerator.cpp.004t.gimple

GKD

./chebyshevAccelerator.o.gkd

OBJ

obj: ./chebyshevAccelerator.o

unassigned

gtrModel.cpp

Class

./gtrModel.cpp.002t.class

Gimple

./gtrModel.cpp.004t.gimple

GKD

./gtrModel.o.gkd

OBJ

obj: ./gtrModel.o

unassigned

fromQtoPt.cpp

Class

./fromQtoPt.cpp.002t.class

Gimple

./fromQtoPt.cpp.004t.gimple

GKD

./fromQtoPt.o.gkd

OBJ

obj: ./fromQtoPt.o

unassigned

distanceTable.cpp

Class

./distanceTable.cpp.002t.class

Gimple

./distanceTable.cpp.004t.gimple

GKD

./distanceTable.o.gkd

OBJ

obj: ./distanceTable.o

unassigned

nj.cpp

Class

./nj.cpp.002t.class

Gimple

./nj.cpp.004t.gimple

GKD

./nj.o.gkd

OBJ

obj: ./nj.o

unassigned

njConstrain.cpp

Class

./njConstrain.cpp.002t.class

Gimple

./njConstrain.cpp.004t.gimple

GKD

./njConstrain.o.gkd

OBJ

obj: ./njConstrain.o

unassigned

numRec.cpp

Class

./numRec.cpp.002t.class

Gimple

./numRec.cpp.004t.gimple

GKD

./numRec.o.gkd

OBJ

obj: ./numRec.o

unassigned

stochasticProcess.cpp

Class

./stochasticProcess.cpp.002t.class

Gimple

./stochasticProcess.cpp.004t.gimple

GKD

./stochasticProcess.o.gkd

OBJ

obj: ./stochasticProcess.o

unassigned

likeDist.cpp

Class

./likeDist.cpp.002t.class

Gimple

./likeDist.cpp.004t.gimple

GKD

./likeDist.o.gkd

OBJ

obj: ./likeDist.o

unassigned

countTableComponent.cpp

Class

./countTableComponent.cpp.002t.class

Gimple

./countTableComponent.cpp.004t.gimple

GKD

./countTableComponent.o.gkd

OBJ

obj: ./countTableComponent.o

unassigned

fastStartTree.cpp

Class

./fastStartTree.cpp.002t.class

Gimple

./fastStartTree.cpp.004t.gimple

GKD

./fastStartTree.o.gkd

OBJ

obj: ./fastStartTree.o

unassigned

bestAlpha.cpp

Class

./bestAlpha.cpp.002t.class

Gimple

./bestAlpha.cpp.004t.gimple

GKD

./bestAlpha.o.gkd

OBJ

obj: ./bestAlpha.o

unassigned

gammaDistribution.cpp

Class

./gammaDistribution.cpp.002t.class

Gimple

./gammaDistribution.cpp.004t.gimple

GKD

./gammaDistribution.o.gkd

OBJ

obj: ./gammaDistribution.o

unassigned

siteSpecificRate.cpp

Class

./siteSpecificRate.cpp.002t.class

Gimple

./siteSpecificRate.cpp.004t.gimple

GKD

./siteSpecificRate.o.gkd

OBJ

obj: ./siteSpecificRate.o

unassigned

likelihoodComputation.cpp

Class

./likelihoodComputation.cpp.002t.class

Gimple

./likelihoodComputation.cpp.004t.gimple

GKD

./likelihoodComputation.o.gkd

OBJ

obj: ./likelihoodComputation.o

unassigned

recognizeFormat.cpp

Class

./recognizeFormat.cpp.002t.class

Gimple

./recognizeFormat.cpp.004t.gimple

GKD

./recognizeFormat.o.gkd

OBJ

obj: ./recognizeFormat.o

unassigned

bblEM.cpp

Class

./bblEM.cpp.002t.class

Gimple

./bblEM.cpp.004t.gimple

GKD

./bblEM.o.gkd

OBJ

obj: ./bblEM.o

unassigned

hky.cpp

Class

./hky.cpp.002t.class

Gimple

./hky.cpp.004t.gimple

GKD

./hky.o.gkd

OBJ

obj: ./hky.o

unassigned

bestGtrModelParams.cpp

Class

./bestGtrModelParams.cpp.002t.class

Gimple

./bestGtrModelParams.cpp.004t.gimple

GKD

./bestGtrModelParams.o.gkd

OBJ

obj: ./bestGtrModelParams.o

unassigned

tamura92.cpp

Class

./tamura92.cpp.002t.class

Gimple

./tamura92.cpp.004t.gimple

GKD

./tamura92.o.gkd

OBJ

obj: ./tamura92.o

unassigned

bestHKYparam.cpp

Class

./bestHKYparam.cpp.002t.class

Gimple

./bestHKYparam.cpp.004t.gimple

GKD

./bestHKYparam.o.gkd

OBJ

obj: ./bestHKYparam.o

unassigned

bestTamura92param.cpp

Class

./bestTamura92param.cpp.002t.class

Gimple

./bestTamura92param.cpp.004t.gimple

GKD

./bestTamura92param.o.gkd

OBJ

obj: ./bestTamura92param.o

talRandom.cpp

Class

./talRandom.cpp.002t.class

Gimple

./talRandom.cpp.004t.gimple

GKD

./talRandom.o.gkd

OBJ

obj: ./talRandom.o

unassigned

fromCountTableComponentToDistance.cpp

Class

./fromCountTableComponentToDistance.cpp.002t.class

Gimple

./fromCountTableComponentToDistance.cpp.004t.gimple

GKD

./fromCountTableComponentToDistance.o.gkd

OBJ

obj: ./fromCountTableComponentToDistance.o

unassigned

computeCounts.cpp

Class

./computeCounts.cpp.002t.class

Gimple

./computeCounts.cpp.004t.gimple

GKD

./computeCounts.o.gkd

OBJ

obj: ./computeCounts.o

unassigned

computeDownAlg.cpp

Class

./computeDownAlg.cpp.002t.class

Gimple

./computeDownAlg.cpp.004t.gimple

GKD

./computeDownAlg.o.gkd

OBJ

obj: ./computeDownAlg.o

unassigned

computeUpAlg.cpp

Class

./computeUpAlg.cpp.002t.class

Gimple

./computeUpAlg.cpp.004t.gimple

GKD

./computeUpAlg.o.gkd

OBJ

obj: ./computeUpAlg.o

unassigned

gammaUtilities.cpp

Class

./gammaUtilities.cpp.002t.class

Gimple

./gammaUtilities.cpp.004t.gimple

GKD

./gammaUtilities.o.gkd

OBJ

obj: ./gammaUtilities.o

unassigned

seqContainerTreeMap.cpp

Class

./seqContainerTreeMap.cpp.002t.class

Gimple

./seqContainerTreeMap.cpp.004t.gimple

GKD

./seqContainerTreeMap.o.gkd

OBJ

obj: ./seqContainerTreeMap.o

unassigned

treeUtil.cpp

Class

./treeUtil.cpp.002t.class

Gimple

./treeUtil.cpp.004t.gimple

GKD

./treeUtil.o.gkd

OBJ

obj: ./treeUtil.o

unassigned

multipleStochasticProcess.cpp

Class

./multipleStochasticProcess.cpp.002t.class

Gimple

./multipleStochasticProcess.cpp.004t.gimple

GKD

./multipleStochasticProcess.o.gkd

OBJ

obj: ./multipleStochasticProcess.o

unassigned

tree.cpp

Class

./tree.cpp.002t.class

Gimple

./tree.cpp.004t.gimple

GKD

./tree.o.gkd

OBJ

obj: ./tree.o

unassigned

bblEMProportionalEB.cpp

Class

./bblEMProportionalEB.cpp.002t.class

Gimple

./bblEMProportionalEB.cpp.004t.gimple

GKD

./bblEMProportionalEB.o.gkd

OBJ

obj: ./bblEMProportionalEB.o

unassigned

fromCountTableComponentToDistancePropEB.cpp

Class

./fromCountTableComponentToDistancePropEB.cpp.002t.class

Gimple

./fromCountTableComponentToDistancePropEB.cpp.004t.gimple

GKD

./fromCountTableComponentToDistancePropEB.o.gkd

OBJ

obj: ./fromCountTableComponentToDistancePropEB.o

unassigned

likeDistPropEB.cpp

Class

./likeDistPropEB.cpp.002t.class

Gimple

./likeDistPropEB.cpp.004t.gimple

GKD

./likeDistPropEB.o.gkd

OBJ

obj: ./likeDistPropEB.o

unassigned

bblLSProportionalEB.cpp

Class

./bblLSProportionalEB.cpp.002t.class

Gimple

./bblLSProportionalEB.cpp.004t.gimple

GKD

./bblLSProportionalEB.o.gkd

OBJ

obj: ./bblLSProportionalEB.o

unassigned

phylipFormat.cpp

Class

./phylipFormat.cpp.002t.class

Gimple

./phylipFormat.cpp.004t.gimple

GKD

./phylipFormat.o.gkd

OBJ

obj: ./phylipFormat.o

unassigned

maseFormat.cpp

Class

./maseFormat.cpp.002t.class

Gimple

./maseFormat.cpp.004t.gimple

GKD

./maseFormat.o.gkd

OBJ

obj: ./maseFormat.o

unassigned

clustalFormat.cpp

Class

./clustalFormat.cpp.002t.class

Gimple

./clustalFormat.cpp.004t.gimple

GKD

./clustalFormat.o.gkd

OBJ

obj: ./clustalFormat.o

unassigned

fastaFormat.cpp

Class

./fastaFormat.cpp.002t.class

Gimple

./fastaFormat.cpp.004t.gimple

GKD

./fastaFormat.o.gkd

OBJ

obj: ./fastaFormat.o

unassigned

phylipSequentialFormat.cpp

Class

./phylipSequentialFormat.cpp.002t.class

Gimple

./phylipSequentialFormat.cpp.004t.gimple

GKD

./phylipSequentialFormat.o.gkd

OBJ

obj: ./phylipSequentialFormat.o

unassigned

molphyFormat.cpp

Class

./molphyFormat.cpp.002t.class

Gimple

./molphyFormat.cpp.004t.gimple

GKD

./molphyFormat.o.gkd

OBJ

obj: ./molphyFormat.o

getRandomWeights.cpp

Class

./getRandomWeights.cpp.002t.class

Gimple

./getRandomWeights.cpp.004t.gimple

GKD

./getRandomWeights.o.gkd

OBJ

obj: ./getRandomWeights.o

unassigned

nexusFormat.cpp

Class

./nexusFormat.cpp.002t.class

Gimple

./nexusFormat.cpp.004t.gimple

GKD

./nexusFormat.o.gkd

OBJ

obj: ./nexusFormat.o

alphabet.cpp

Class

./alphabet.cpp.002t.class

Gimple

./alphabet.cpp.004t.gimple

GKD

./alphabet.o.gkd

OBJ

obj: ./alphabet.o

unassigned

readTree.cpp

Class

./readTree.cpp.002t.class

Gimple

./readTree.cpp.004t.gimple

GKD

./readTree.o.gkd

OBJ

obj: ./readTree.o

unassigned

computePijComponent.cpp

Class

./computePijComponent.cpp.002t.class

Gimple

./computePijComponent.cpp.004t.gimple

GKD

./computePijComponent.o.gkd

OBJ

obj: ./computePijComponent.o

unassigned

unObservableData.cpp

Class

./unObservableData.cpp.002t.class

Gimple

./unObservableData.cpp.004t.gimple

GKD

./unObservableData.o.gkd

OBJ

obj: ./unObservableData.o

unassigned

likelihoodComputationGL.cpp

Class

./likelihoodComputationGL.cpp.002t.class

Gimple

./likelihoodComputationGL.cpp.004t.gimple

GKD

./likelihoodComputationGL.o.gkd

OBJ

obj: ./likelihoodComputationGL.o

includes

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

rate4siteOptions.cpp

../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./rate4siteOptions.h ../headers/../../src/phylogeny/errorMsg.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers/../../src/phylogeny/getopt.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers/../../src/phylogeny/stochasticProcess.h ../headers/../../src/phylogeny/generalGammaDistribution.h ../headers/../../src/phylogeny/nucJC.h ../headers/../../src/phylogeny/aaJC.h ../headers/../../src/phylogeny/trivialAccelerator.h ../headers/../../src/phylogeny/jcDistance.h ../headers/../../src/phylogeny/tree.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers/../../src/phylogeny/computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers/../../src/phylogeny/gammaDistribution.h

rate4site.cpp

../headers/../../src/phylogeny/sequence.h ../headers/../../src/phylogeny/sequenceContainer.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/streambuf ../headers/../../src/phylogeny/logFile.h ../headers//usr/include/c++/4.9/iomanip ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers/../../src/phylogeny/nj.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers/../../src/phylogeny/uniDistribution.h ../headers/../../src/phylogeny/readDatMatrix.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers/../../src/phylogeny/bblEM.h ../headers//usr/include/c++/4.9/istream ../headers/../../src/phylogeny/definitions.h ../headers//usr/include/c++/4.9/iostream ../headers/../../src/phylogeny/likeDist.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/stl_tree.h ../headers//usr/include/c++/4.9/bits/stl_pair.h ../headers//usr/include/c++/4.9/bits/stl_function.h ../headers//usr/include/c++/4.9/bits/stl_map.h ../headers//usr/include/c++/4.9/ctime ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/typeinfo ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers/../../src/phylogeny/doubleRep.h ../headers//usr/include/wctype.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./rate4siteOptions.h ../headers/../../src/phylogeny/alphabet.h ../headers/../../src/phylogeny/errorMsg.h ../headers/../../src/phylogeny/someUtil.h ../headers/../../src/phylogeny/mulAlphabet.h ../headers/../../src/phylogeny/readTree.h ../headers/../../src/phylogeny/geneticCodeHolder.h ../headers/../../src/phylogeny/codon.h ../headers/../../src/phylogeny/evaluateCharacterFreq.h ../headers/../../src/phylogeny/datMatrixHolder.h ../headers/../../src/phylogeny/njConstrain.h ../headers/../../src/phylogeny/distances2Tree.h ../headers/../../src/phylogeny/numRec.h ../headers/../../src/phylogeny/suffStatComponent.h ../headers/../../src/phylogeny/likelihoodComputation.h ../headers/../../src/phylogeny/checkcovFanctors.h ../headers/../../src/phylogeny/countTableComponent.h ../headers/../../src/phylogeny/unObservableData.h ../headers/../../src/phylogeny/fastStartTree.h ../headers/../../src/phylogeny/checkcovFanctorsWithFactors.h ../headers/../../src/phylogeny/bestAlpha.h ../headers/../../src/phylogeny/recognizeFormat.h ../headers/../../src/phylogeny/bestGtrModelParams.h ../headers/../../src/phylogeny/bestHKYparam.h ../headers/../../src/phylogeny/bestTamura92param.h ./rate4site.h ../headers/../../src/phylogeny/gainLossAlphabet.h ../headers/../../src/phylogeny/distanceMethod.h ../headers/../../src/phylogeny/pijAccelerator.h ../headers/../../src/phylogeny/replacementModel.h ../headers/../../src/phylogeny/nucleotide.h ../headers/../../src/phylogeny/amino.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers/../../src/phylogeny/distribution.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h ../headers/../../src/phylogeny/siteSpecificRate.h ../headers/../../src/phylogeny/distanceTable.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./gainLossAlphabet.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

sequenceContainer.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./sequence.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

sequence.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_algo.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/bits/vector.tcc ./sequence.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./mulAlphabet.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./mulAlphabet.h

mulAlphabet.cpp

../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ./alphabet.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ./errorMsg.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./someUtil.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/stl_algo.h

someUtil.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/cmath ../headers//usr/include/i386-linux-gnu/bits/mathinline.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/stdlib.h ../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./talRandom.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stream_iterator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./logFile.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/bits/stl_heap.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/iostream ./definitions.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/ctime ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./errorMsg.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/fcntl-linux.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h ../headers//usr/include/ctype.h ../headers//usr/include/dirent.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

logFile.cpp

./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/basic_file.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++io.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/i386-linux-gnu/bits/pthreadtypes.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./errorMsg.h ../headers//usr/include/c++/4.9/new

pijAccelerator.cpp

./definitions.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ./pijAccelerator.h ../headers//usr/include/c++/4.9/new

replacementModel.cpp

./definitions.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ./replacementModel.h ../headers//usr/include/c++/4.9/new

distribution.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./distribution.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

errorMsg.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ostream ./logFile.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h

unassigned

./nucleotide.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h

nucleotide.cpp

../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/char_traits.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ./alphabet.h ../headers//usr/include/wctype.h ./errorMsg.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./amino.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

amino.cpp

../headers//usr/include/c++/4.9/bits/stl_tree.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_pair.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_function.h ../headers//usr/include/c++/4.9/bits/stl_map.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ./geneticCodeHolder.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./codon.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./gainLossAlphabet.h

evaluateCharacterFreq.cpp

./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/iostream ./definitions.h ../headers//usr/include/libio.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./evaluateCharacterFreq.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./sequence.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h

unassigned

./uniDistribution.h

uniDistribution.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ./distribution.h ../headers//usr/include/c++/4.9/new

unassigned

./generalGammaDistribution.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

generalGammaDistribution.cpp

../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./numRec.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./distribution.h ./gammaUtilities.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./readDatMatrix.h ../headers//usr/include/c++/4.9/bits/stl_vector.h

readDatMatrix.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/sstream ./fromQtoPt.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/libio.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/bits/istream.tcc ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/sstream.tcc ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./datMatrixHolder.h ./errorMsg.h ./replacementModel.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

./datMatrixHolder.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

datMatrixHolder.cpp

../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h

unassigned

./chebyshevAccelerator.h

chebyshevAccelerator.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./definitions.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ./pijAccelerator.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

./gtrModel.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

gtrModel.cpp

../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./fromQtoPt.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./datMatrixHolder.h ./readDatMatrix.h ./errorMsg.h ./logFile.h ./matrixUtils.h ./replacementModel.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

./fromQtoPt.h ../headers//usr/include/c++/4.9/bits/stl_vector.h

fromQtoPt.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./numRec.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./matrixUtils.h ./replacementModel.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h ../headers//usr/include/assert.h

unassigned

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h

distanceTable.cpp

./sequenceContainer.h ./sequence.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./distanceMethod.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./nj.h ./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

nj.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_tree.h ../headers//usr/include/c++/4.9/bits/stl_algo.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/bits/stl_pair.h ../headers//usr/include/c++/4.9/bits/stl_map.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_function.h ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./njConstrain.h ./distances2Tree.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ./treeUtil.h ../headers//usr/include/assert.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

njConstrain.cpp

../headers//usr/include/c++/4.9/bits/stl_tree.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/stl_pair.h ../headers//usr/include/c++/4.9/bits/stl_map.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/stl_function.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ./sequence.h ./readTree.h ./njConstrain.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

numRec.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h ../headers//usr/include/c++/4.9/cmath ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_algo.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/bits/stl_heap.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/iostream ./definitions.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./numRec.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./matrixUtils.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h ../headers//usr/include/assert.h

unassigned

./stochasticProcess.h

stochasticProcess.cpp

./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./gainLossAlphabet.h ./likeDist.h ./jcDistance.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./countTableComponent.h ../headers//usr/include/c++/4.9/bits/stl_vector.h

likeDist.cpp

./sequence.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./numRec.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/typeinfo ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ./mulAlphabet.h ./readTree.h ./tree.h ./computePijComponent.h ./unObservableData.h ./distanceMethod.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

countTableComponent.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./countTableComponent.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./gainLossAlphabet.h ./jcDistance.h ./tree.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./bblEM.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_algo.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/bits/stl_heap.h ../headers//usr/include/c++/4.9/bits/move.h

fastStartTree.cpp

../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./logFile.h ./likeDist.h ./sequenceContainer.h ./nj.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/typeinfo ../headers//usr/include/c++/4.9/new ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./mulAlphabet.h ./sequence.h ./fastStartTree.h ./countTableComponent.h ./suffStatComponent.h ./unObservableData.h ./getRandomWeights.h ./njConstrain.h ./distances2Tree.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ./likelihoodComputation.h ./distanceMethod.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h ./treeUtil.h ./distanceTable.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./multipleStochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./generalGammaDistribution.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./gammaDistribution.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./numRec.h ./bestAlpha.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h

bestAlpha.cpp

./bblEM.h ./bblEMProportionalEB.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./sequence.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/iostream ./definitions.h ./sequenceContainer.h ../headers//usr/include/libio.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./tree.h ./alphabet.h ./someUtil.h ./suffStatComponent.h ./countTableComponent.h ./unObservableData.h ./bblLSProportionalEB.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./likelihoodComputation.h

unassigned

./generalGammaDistribution.h ../headers//usr/include/c++/4.9/bits/stl_vector.h

gammaDistribution.cpp

./gammaDistribution.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./numRec.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ./gammaUtilities.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./generalGammaDistribution.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

siteSpecificRate.cpp

./logFile.h ../headers//usr/include/c++/4.9/ostream ./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./numRec.h ./checkcovFanctors.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./suffStatComponent.h ./likelihoodComputation.h ./unObservableData.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h ../headers//usr/include/assert.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./gainLossAlphabet.h ./stochasticProcess.h ./generalGammaDistribution.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

likelihoodComputation.cpp

./suffStatComponent.h ./sequenceContainer.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./logFile.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./tree.h ./alphabet.h ./someUtil.h ./sequence.h ./computeUpAlg.h ./numRec.h ./likelihoodComputation.h ./unObservableData.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./gammaUtilities.h ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./sequence.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h

recognizeFormat.cpp

./definitions.h ../headers//usr/include/c++/4.9/iostream ./sequenceContainer.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./recognizeFormat.h ./maseFormat.h ./molphyFormat.h ./phylipFormat.h ./nexusFormat.h ./fastaFormat.h ./clustalFormat.h ./phylipSequentialFormat.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./gainLossAlphabet.h ./tree.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

bblEM.cpp

./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./treeIt.h ./countTableComponent.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./suffStatComponent.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/ctime ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./bblEM.h ./unObservableData.h ./likelihoodComputation.h ./computeUpAlg.h ./computeDownAlg.h ./computeCounts.h ./fromCountTableComponentToDistance.h ../headers//usr/include/c++/4.9/new

unassigned

./hky.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

hky.cpp

../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./replacementModel.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./multipleStochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./generalGammaDistribution.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/char_traits.h ./numRec.h ./bestGtrModelParams.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./bestAlpha.h

bestGtrModelParams.cpp

./bblEM.h ./bblEMProportionalEB.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./sequence.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./sequenceContainer.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./tree.h ./alphabet.h ./someUtil.h ./suffStatComponent.h ./gtrModel.h ./countTableComponent.h ./unObservableData.h ./bblLSProportionalEB.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./likelihoodComputation.h

unassigned

./tamura92.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

tamura92.cpp

../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./replacementModel.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./multipleStochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./generalGammaDistribution.h ./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./numRec.h ./bestHKYparam.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h

bestHKYparam.cpp

./bblEM.h ./bestAlpha.h ./bblEMProportionalEB.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./sequence.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./sequenceContainer.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./suffStatComponent.h ./countTableComponent.h ./unObservableData.h ./bblLSProportionalEB.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./hky.h ./likelihoodComputation.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./multipleStochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./generalGammaDistribution.h ./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./numRec.h ./bestTamura92param.h ./tamura92.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h

bestTamura92param.cpp

./bblEM.h ./bestAlpha.h ./bblEMProportionalEB.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./sequence.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./sequenceContainer.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./suffStatComponent.h ./countTableComponent.h ./unObservableData.h ./bblLSProportionalEB.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./likelihoodComputation.h

talRandom.cpp

./talRandom.h ../headers//usr/include/c++/4.9/iostream ./definitions.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/ctime ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

./gainLossAlphabet.h ./jcDistance.h ../headers//usr/include/c++/4.9/bits/stl_vector.h

fromCountTableComponentToDistance.cpp

./likeDist.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/typeinfo ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./countTableComponent.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./tree.h ./alphabet.h ./someUtil.h ./mulAlphabet.h ./sequence.h ./computePijComponent.h ./fromCountTableComponentToDistance.h ./unObservableData.h ./distanceMethod.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

./stochasticProcess.h

computeCounts.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./suffStatComponent.h ./computePijComponent.h ./countTableComponent.h ./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./sequence.h ./readTree.h ./tree.h ./computeCounts.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h

unassigned

./stochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./treeIt.h ./tree.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./suffStatComponent.h

computeDownAlg.cpp

./computePijComponent.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./alphabet.h ./someUtil.h ./sequence.h ./computeDownAlg.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./treeIt.h ./tree.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./suffStatComponent.h

computeUpAlg.cpp

./seqContainerTreeMap.h ./sequenceContainer.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./computePijComponent.h ./computeUpAlg.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

gammaUtilities.cpp

../headers//usr/include/i386-linux-gnu/bits/mathinline.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./numRec.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ./gammaUtilities.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

seqContainerTreeMap.cpp

../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./treeIt.h ./tree.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./sequenceContainer.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./treeUtil.h

unassigned

./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

treeUtil.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./treeIt.h ./logFile.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/bits/stl_tree.h ../headers//usr/include/stdlib.h ../headers//usr/include/c++/4.9/bits/stl_pair.h ../headers//usr/include/c++/4.9/bits/stl_algo.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/stl_heap.h ../headers//usr/include/c++/4.9/bits/stl_map.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/basic_file.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++io.h ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_function.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/i386-linux-gnu/bits/pthreadtypes.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/ctype.h

unassigned

./multipleStochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

multipleStochasticProcess.cpp

../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ./stochasticProcess.h ../headers//usr/include/wctype.h ./errorMsg.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

tree.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./tree.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/iomanip ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algo.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/basic_file.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++io.h ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/ctime ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/i386-linux-gnu/bits/pthreadtypes.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/assert.h ./treeUtil.h

unassigned

./stochasticProcess.h ./gainLossAlphabet.h ./multipleStochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./generalGammaDistribution.h ./tree.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

bblEMProportionalEB.cpp

./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./countTableComponent.h ./suffStatComponent.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./treeIt.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/ctime ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./bblEM.h ./bblEMProportionalEB.h ./likelihoodComputation.h ./computeUpAlg.h ./computeDownAlg.h ./computeCounts.h ./fromCountTableComponentToDistancePropEB.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./fromCountTableComponentToDistance.h ../headers//usr/include/assert.h

unassigned

./likeDistPropEB.h

fromCountTableComponentToDistancePropEB.cpp

./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./countTableComponent.h ./errorMsg.h ./fromCountTableComponentToDistancePropEB.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./multipleStochasticProcess.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./generalGammaDistribution.h ./countTableComponent.h ./numRec.h ./likeDistPropEB.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

likeDistPropEB.cpp

./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./numRec.h ./bblLSProportionalEB.h ./tree.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/i386-linux-gnu/bits/mathinline.h

bblLSProportionalEB.cpp

./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./suffStatComponent.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./likelihoodComputation.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

phylipFormat.cpp

./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./logFile.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ./sequence.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ./phylipFormat.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

maseFormat.cpp

../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ./sequenceContainer.h ./logFile.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ./sequence.h ./maseFormat.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

clustalFormat.cpp

../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_pair.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_tree.h ../headers//usr/include/c++/4.9/bits/char_traits.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/stl_map.h ./sequence.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/stl_function.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./clustalFormat.h ./geneticCodeHolder.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

fastaFormat.cpp

../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./logFile.h ./ConversionUtils.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ./sequence.h ./sequenceContainer.h ./fastaFormat.h ../headers//usr/include/stdlib.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-float.h ../headers//usr/include/i386-linux-gnu/bits/stdlib-bsearch.h ../headers//usr/include/i386-linux-gnu/bits/stdlib.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

phylipSequentialFormat.cpp

./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./logFile.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./someUtil.h ./sequence.h ./phylipSequentialFormat.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

molphyFormat.cpp

./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./sequence.h ./molphyFormat.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

getRandomWeights.cpp

./talRandom.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/ctime ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ./getRandomWeights.h ../headers//usr/include/wctype.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./gainLossAlphabet.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

nexusFormat.cpp

../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_pair.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_tree.h ../headers//usr/include/c++/4.9/bits/char_traits.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/bits/stl_construct.h ./sequence.h ../headers//usr/include/c++/4.9/bits/stl_map.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/stl_function.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./alphabet.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./someUtil.h ./nexusFormat.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new

alphabet.cpp

../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ./alphabet.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

readTree.cpp

../headers//usr/include/c++/4.9/bits/stl_iterator.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./readTree.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/ctype.h

unassigned

./stochasticProcess.h ./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./treeIt.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h

computePijComponent.cpp

./logFile.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./errorMsg.h ./readTree.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h

unassigned

./stochasticProcess.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

unObservableData.cpp

../headers//usr/include/c++/4.9/bits/stl_algobase.h ./sequenceContainer.h ../headers//usr/include/c++/4.9/bits/vector.tcc ./sequence.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./suffStatComponent.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ./unObservableData.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./logFile.h ./tree.h ./alphabet.h ./someUtil.h ./computeUpAlg.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ./likelihoodComputation.h ./likelihoodComputationGL.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h ./stochasticProcess.h ./gainLossAlphabet.h ./tree.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./computePijComponent.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h

likelihoodComputationGL.cpp

./sequenceContainer.h ./suffStatComponent.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.h ./logFile.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./definitions.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/c++config.h ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/basic_string.tcc ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/bits/ostream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/c++/4.9/bits/predefined_ops.h ../headers//usr/include/c++/4.9/ext/numeric_traits.h ../headers//usr/include/c++/4.9/ext/alloc_traits.h ../headers//usr/include/c++/4.9/ext/type_traits.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/i386-linux-gnu/bits/wchar2.h ../headers//usr/include/time.h ../headers//usr/include/locale.h ../headers//usr/include/i386-linux-gnu/bits/types.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/atomic_word.h ../headers//usr/include/wctype.h ./readTree.h ./errorMsg.h ../headers//usr/include/_G_config.h ../headers//usr/include/i386-linux-gnu/bits/stdio2.h ../headers//usr/include/i386-linux-gnu/bits/stdio.h ./alphabet.h ./someUtil.h ./sequence.h ./computeUpAlg.h ./likelihoodComputationGL.h ./unObservableData.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/32/bits/gthr-default.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/assert.h ../headers//usr/include/i386-linux-gnu/bits/mathcalls.h