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text data/fastml-3.11/libs/phylogeny/gtrModel.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/gammaDistribution.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/codonUtils.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/generalGammaDistribution.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/alphabet.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/NNiProp.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/splitMap.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/fromCountTableComponentToDistanceProp.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/simulateJumpsAbstract.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/split.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/readDatMatrix.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/recognizeFormat.cpp: C source, ASCII text 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data/fastml-3.11/libs/phylogeny/phylipSequentialFormat.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/bblEMSeperate.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/simulateRateShiftJumps.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/matrixUtils.cpp: C source, ASCII text, with CRLF, LF line terminators data/fastml-3.11/libs/phylogeny/unObservableData.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/likelihoodComputationFactors.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/computeDownAlg.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/distanceBasedSeqs2Tree.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/logRep.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/tree.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/bblEMProportionalEB.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/treeIt.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/getopt.c: C source, ASCII text data/fastml-3.11/libs/phylogeny/HIVw.dat.q: ASCII text data/fastml-3.11/libs/phylogeny/distanceTable.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/treeUtil.h: C source, ASCII text data/fastml-3.11/libs/phylogeny/mulAlphabet.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/getopt.h: C source, ASCII text data/fastml-3.11/libs/phylogeny/nucJC.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/stochasticProcess.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/ussrvModel.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/gtrModel.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/searchStatus.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/bblEMSeperate.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/givenRatesMLDistance.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/gainLossAlphabet.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/replacementModel.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/bestParamUSSRV.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/talRandom.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/clustalFormat.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/suffStatGammaMixture.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/njConstrain.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/bestHKYparam.cpp: C++ source, ASCII text, with CRLF, LF line terminators data/fastml-3.11/libs/phylogeny/samplingSequences.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/mixtureDistribution.cpp: C source, ASCII text, with CRLF, LF line terminators data/fastml-3.11/libs/phylogeny/fromQtoPt.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/bblEMfixRoot.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/fromCountTableComponentToDistancePropEB.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/phylogeny.suo: Composite Document File V2 Document, Cannot read section info data/fastml-3.11/libs/phylogeny/replacementModelSSRV.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/stochasticProcess.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/ussrvModel.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/tamura92.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/evaluateCharacterFreq.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/distanceTable.h: C source, ASCII text data/fastml-3.11/libs/phylogeny/gammaDistributionFixedCategories.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/givenRatesMLDistance.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/generalGammaDistributionLaguerre.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/HIVb.dat.q: ASCII text data/fastml-3.11/libs/phylogeny/C_evalParamUSSRV.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/cpREV45.dat.q: ASCII text data/fastml-3.11/libs/phylogeny/bblLSProportionalEB.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/extremeValDistribution.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/libs/phylogeny/likeDist2Codon.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/distances2Tree.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/findRateOfGene.h: C source, ASCII text data/fastml-3.11/libs/phylogeny/bblEM.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/allTreesSeparateModel.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/mtREV24.dat.q: ASCII text data/fastml-3.11/libs/phylogeny/countTableComponent.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/bestAlphaAndNu.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/Nni.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/granthamChemicalDistances.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/fromCountTableComponentToDistance.h: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/fromQtoPt.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/evolObjs.args: ASCII text data/fastml-3.11/libs/phylogeny/make.dep: ASCII text data/fastml-3.11/libs/phylogeny/#Makefile#: C source, ASCII text data/fastml-3.11/libs/phylogeny/likeDist.cpp: C++ source, ASCII text data/fastml-3.11/libs/phylogeny/numRec.cpp: C source, ASCII text data/fastml-3.11/libs/phylogeny/likeDistfixRoot.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/bblLS.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/runPerlReadSimResAllModels.PerBranchAndPerPos.andMP.TarRm.Bash: Bourne-Again shell script, ASCII text executable data/fastml-3.11/programs/gainLoss/gainLossOptions.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLossModel.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLoss.vcproj: XML 1.0 document, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/optimizeGainLossModelVV.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/siteSpecificGL.h: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/junk.txt: C source, ASCII text, with very long lines, with CRLF, LF line terminators data/fastml-3.11/programs/gainLoss/gainLossUtils.h: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLossProject.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/simulateOnePos.cpp: C++ source, ASCII text, with CRLF line terminators 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data/fastml-3.11/programs/gainLoss/rate4site.gainLossFunctions.txt: ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/simulateOnePos.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/simulateChangesAlongTree.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/optimizeGainLossModel.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLossOptimizer.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/computePosteriorExpectationOfChange.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLoss.h: C++ source, ASCII text, with very long lines, with CRLF line terminators data/fastml-3.11/programs/gainLoss/classesInherit.costurs.clone.assignment.txt: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLossAlphabet.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/LpostPerCat.PerSp.txt: ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/LOG: cannot open `data/fastml-3.11/programs/gainLoss/LOG' (No such file or directory) chages.txt: cannot open `chages.txt' (No such file or directory) data/fastml-3.11/programs/gainLoss/computeCountsGL.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/ancestralReconstructStates.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/rate4siteGL.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLoss4site.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/make.dep: ASCII text data/fastml-3.11/programs/gainLoss/computeCorrelations.cpp: C source, Non-ISO extended-ASCII text, with CRLF line terminators data/fastml-3.11/programs/gainLoss/gainLoss.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/fastml/bb_options.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/computeMarginalReconstruction.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/sequenceDataDiff.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbComputeDownAlg.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbfindBestAVDynProg.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bb_options.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbEvaluateSpecificAV.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/bbAlg.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/fastml.vcproj: XML 1.0 document, ASCII text, with CRLF line terminators data/fastml-3.11/programs/fastml/bbNodeOrderAlg.cpp: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbComputeUpAlg.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/bbEvaluateSpecificAV.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbAlg.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbNodeOrderAlg.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbComputeUpAlg.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbReport.cpp: C++ source, ASCII text data/fastml-3.11/programs/fastml/jointNoGamma.cpp: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbReport.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/fastml.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/suffStatComponentJointNoGamma.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/jointNoGamma.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/computeMarginalReconstruction.cpp: C++ source, ASCII text data/fastml-3.11/programs/fastml/sequenceDataDiff.cpp: C++ source, ASCII text data/fastml-3.11/programs/fastml/suffStatComponentJointNoGamma.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/bbComputeDownAlg.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/Makefile: a /usr/local/bin/gmake script, ASCII text executable data/fastml-3.11/programs/fastml/bbfindBestAVDynProg.cpp: C source, ASCII text data/fastml-3.11/programs/fastml/mainbb.h: C++ source, ASCII text data/fastml-3.11/programs/fastml/make.dep: ASCII text data/fastml-3.11/programs/fastml/mainbb.cpp: C++ source, ASCII text data/fastml-3.11/programs/fastml/bb_options_list.h: C++ source, ASCII text data/fastml-3.11/programs/indelCoder/indelCoderUtils.h: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/gaps.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/indelCoderProject.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/character.h: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/indelCoder.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/indelCoder.h: C++ source, Non-ISO extended-ASCII text, with CRLF, LF line terminators data/fastml-3.11/programs/indelCoder/indelCoderOptions.cpp: C++ source, ASCII text, with CRLF, LF line terminators data/fastml-3.11/programs/indelCoder/indelCoder.vcproj: XML 1.0 document, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/indelCoderOptions.h: C++ source, ASCII text data/fastml-3.11/programs/indelCoder/indelCoderUtils.cpp: C source, ASCII text, with CRLF, LF line terminators data/fastml-3.11/programs/indelCoder/gaps.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/Makefile: a /usr/local/bin/gmake script, ASCII text executable data/fastml-3.11/programs/indelCoder/character.cpp: C source, ASCII text, with CRLF line terminators data/fastml-3.11/programs/indelCoder/make.dep: ASCII text data/fastml-3.11/programs/Makefile: ASCII text data/fastml-3.11/programs/Makefile.generic: makefile script, ASCII text data/fastml-3.11/Makefile: makefile script, ASCII text data/fastml-3.11/README: ASCII text data/fastml-3.11/debian/changelog: UTF-8 Unicode text data/fastml-3.11/debian/compat: ASCII text data/fastml-3.11/debian/control: ASCII text data/fastml-3.11/debian/copyright: ASCII text data/fastml-3.11/debian/createmanpages: POSIX shell script, ASCII text executable data/fastml-3.11/debian/fastml.1: troff or preprocessor input, ASCII text data/fastml-3.11/debian/gainLoss.1: troff or preprocessor input, ASCII text data/fastml-3.11/debian/indelCoder.1: troff or preprocessor input, ASCII text data/fastml-3.11/debian/install: ASCII text data/fastml-3.11/debian/manpages: ASCII text data/fastml-3.11/debian/patches/change_to_tests_dir_only_if_existing.patch: unified diff output, ASCII text data/fastml-3.11/debian/patches/cross.patch: unified diff output, ASCII text data/fastml-3.11/debian/patches/fix_intall_target.patch: unified diff output, ASCII text data/fastml-3.11/debian/patches/fix_makefile4test.patch: unified diff output, ASCII text data/fastml-3.11/debian/patches/gcc_5.patch: unified diff output, ASCII text data/fastml-3.11/debian/patches/remove-template-depth.patch: unified diff output, ASCII text data/fastml-3.11/debian/patches/series: ASCII text data/fastml-3.11/debian/patches/skip_failing_tests.patch: unified diff output, ASCII text data/fastml-3.11/debian/patches/spelling.patch: unified diff output, ASCII text, with CRLF, LF line terminators data/fastml-3.11/debian/rules: a /usr/bin/make -f script, ASCII text executable data/fastml-3.11/debian/source/format: ASCII text data/fastml-3.11/debian/upstream/metadata: UTF-8 Unicode text data/fastml-3.11/debian/watch: ASCII text data/fastml-3.11/.pc/.version: ASCII text data/fastml-3.11/.pc/.quilt_patches: ASCII text data/fastml-3.11/.pc/.quilt_series: ASCII text data/fastml-3.11/.pc/applied-patches: ASCII text data/fastml-3.11/.pc/gcc_5.patch/libs/phylogeny/tests/readTreeWithComments.cpp: C++ source, ASCII text data/fastml-3.11/.pc/fix_makefile4test.patch/libs/phylogeny/tests/Makefile: makefile script, ASCII text data/fastml-3.11/.pc/fix_intall_target.patch/programs/Makefile.generic: makefile script, ASCII text data/fastml-3.11/.pc/spelling.patch/libs/phylogeny/likeDist.cpp: C++ source, ASCII text data/fastml-3.11/.pc/spelling.patch/libs/phylogeny/numRec.cpp: C source, ASCII text data/fastml-3.11/.pc/spelling.patch/libs/phylogeny/likeDistfixRoot.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/.pc/spelling.patch/programs/fastml/mainbb.cpp: C++ source, ASCII text data/fastml-3.11/.pc/spelling.patch/programs/fastml/bb_options_list.h: C++ source, ASCII text data/fastml-3.11/.pc/spelling.patch/programs/gainLoss/computeCorrelations.cpp: C source, Non-ISO extended-ASCII text, with CRLF line terminators data/fastml-3.11/.pc/spelling.patch/programs/gainLoss/gainLoss.cpp: C++ source, ASCII text, with CRLF line terminators data/fastml-3.11/.pc/change_to_tests_dir_only_if_existing.patch/programs/Makefile.generic: makefile script, ASCII text data/fastml-3.11/.pc/skip_failing_tests.patch/libs/phylogeny/tests/Makefile: makefile script, ASCII text data/fastml-3.11/.pc/remove-template-depth.patch/libs/phylogeny/tests/Makefile: C source, ASCII text data/fastml-3.11/.pc/cross.patch/programs/Makefile.generic: makefile script, ASCII text