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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/fastml">Debian Med / fastml</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad">05b00510</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-07-19T18:15:39Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.11</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#038969f71364453d51878b478b038d1964c8c1ff">
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+
libs/phylogeny/#Makefile#
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<li class="file-stats">
<a href="#d0d2651a62d3379d9fd010fb694608d67975a0e6">
libs/phylogeny/Makefile
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<li class="file-stats">
<a href="#f5773c791126ed6431e527cdccc7c8e5267e0db0">
libs/phylogeny/errorMsg.cpp
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<li class="file-stats">
<a href="#ff44631b544f16a02b54dd833bb74ed471f67c9c">
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libs/phylogeny/make.dep
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<li class="file-stats">
<a href="#678cc88c16875a978296761818f173170fc6e7e2">
libs/phylogeny/someUtil.cpp
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<li class="file-stats">
<a href="#0007d31d42c492deef7cdbecee9f101624baedb5">
programs/Makefile.generic
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<li class="file-stats">
<a href="#179fb1eeb60770928e6ec5fcc14eca2655108e6d">
programs/fastml/bbReport.cpp
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<li class="file-stats">
<a href="#239a1f618d88854b9554db94a08a5737bdc9bc85">
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programs/fastml/make.dep
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<li class="file-stats">
<a href="#e3ae4d8826cc1b107e6e2dafc15891afd34309fc">
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programs/gainLoss/make.dep
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<li class="file-stats">
<a href="#8666366720e38d2d816682f2ebaca796912d92dc">
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programs/indelCoder/make.dep
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<h4>Changes:</h4>
<li id="038969f71364453d51878b478b038d1964c8c1ff">
<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#038969f71364453d51878b478b038d1964c8c1ff"><strong>libs/phylogeny/#Makefile#</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#! /usr/local/bin/gmake</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># $Id: Makefile 11759 2013-09-24 13:45:40Z elilevy $</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># makfile for yaep5</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># use LOGREP=t or DOUBLEREP=t to activate logRep or doubleRep respectively (or setenv DOUBLEREP in the shell)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">#DOUBLEREP=t</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">#LOGREP=t</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Libsources= AddLog.cpp NNiProp.cpp NNiSep.cpp Nni.cpp aaJC.cpp \</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> allTrees.cpp allTreesSeparateModel.cpp alphabet.cpp amino.cpp \</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> bestAlpha.cpp bestAlphaManyTrees.cpp bestHKYparam.cpp bootstrap.cpp \</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> bblEM.cpp bblEMfixRoot.cpp bblEMProprtional.cpp bblEMProportionalEB.cpp bblLSProportionalEB.cpp bblEMSeperate.cpp \</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> chebyshevAccelerator.cpp clustalFormat.cpp codon.cpp codonJC.cpp \</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> computeCounts.cpp computeDownAlg.cpp computeMarginalAlg.cpp \</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> computePijComponent.cpp computeUpAlg.cpp computeUpAlgFactors.cpp \</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> computeSubstitutionCounts.cpp \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions.cpp \</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ConversionUtils.cpp countTableComponent.cpp datMatrixHolder.cpp distanceTable.cpp \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> distribution.cpp errorMsg.cpp evaluateCharacterFreq.cpp \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> fastStartTree.cpp fastaFormat.cpp findRateOfGene.cpp \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> fromCountTableComponentToDistance.cpp fromCountTableComponentToDistancefixRoot.cpp \</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> fromCountTableComponentToDistanceProp.cpp fromCountTableComponentToDistancePropEB.cpp fromQtoPt.cpp \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> generalGammaDistributionFixedCategories.cpp gammaDistribution.cpp gammaUtilities.cpp \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> generalGammaDistribution.cpp getRandomWeights.cpp goldmanYangModel.cpp \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> granthamChemicalDistances.cpp hky.cpp simulateWithDependence.cpp KH_calculation.cpp likeDist.cpp likeDistfixRoot.cpp \</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> likeDistProp.cpp likeDistPropEB.cpp likelihoodComputation.cpp \</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> likelihoodComputationFactors.cpp logFile.cpp maseFormat.cpp \</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> molphyFormat.cpp nexusFormat.cpp nj.cpp njConstrain.cpp \</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> nucJC.cpp nucleotide.cpp numRec.cpp Parameters.cpp phylipFormat.cpp \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> pijAccelerator.cpp readDatMatrix.cpp readTree.cpp recognizeFormat.cpp \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> replacementModel.cpp searchStatus.cpp seqContainerTreeMap.cpp \</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> sequence.cpp sequenceContainer.cpp simulateTree.cpp \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> siteSpecificRate.cpp someUtil.cpp split.cpp splitMap.cpp \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> splitTreeUtil.cpp stochasticProcess.cpp suffStatComponent.cpp \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> talRandom.cpp tree.cpp treeIt.cpp treeUtil.cpp uniDistribution.cpp \</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> uniformDistribution.cpp cmdline2EvolObjs.cpp \</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> generalGammaDistributionLaguerre.cpp gammaDistributionLaguerre.cpp GLaguer.cpp \</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> givenRatesMLDistance.cpp distanceBasedSeqs2Tree.cpp \</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> posteriorDistance.cpp pairwiseGammaDistance.cpp doubleRep.cpp \</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> logRep.cpp indel.cpp indelModel.cpp mulAlphabet.cpp \</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> replacementModelSSRV.cpp stochasticProcessSSRV.cpp bestAlphaAndNu.cpp \</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> C_evalParamUSSRV.cpp matrixUtils.cpp betaOmegaDistribution.cpp \</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> betaUtilities.cpp betaDistribution.cpp geneticCodeHolder.cpp \</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> samplingSequences.cpp bblEM2USSRV.cpp bestParamUSSRV.cpp \</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> likeDist2USSRV.cpp ussrvModel.cpp likelihoodComputation2USSRV.cpp \</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> fromCountTableComponentToDistance2USSRV.cpp normalDist.cpp \</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> tamura92.cpp bestTamura92param.cpp phylipSequentialFormat.cpp \</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> simulateCodonsJumps.cpp \</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> simulateJumpsAbstract.cpp \</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> ssrvDistanceSeqs2Tree.cpp multipleStochasticProcess.cpp distributionPlusInvariant.cpp\</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> extremeValDistribution.cpp \</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> gammaDistributionFixedCategories.cpp generalGammaDistributionPlusInvariant.cpp gammaDistributionPlusInvariant.cpp \</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> distributionPlusCategory.cpp simulateJumps.cpp computeJumps.cpp seqeuncesFilter.cpp \</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> optGammaMixtureLS.cpp mixtureDistribution.cpp suffStatGammaMixture.cpp GamMixtureOptimizer.cpp optGammaMixtureEM.cpp gainLossAlphabet.cpp \</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> wYangModel.cpp codonUtils.cpp likelihoodComputation2Codon.cpp likeDist2Codon.cpp unObservableData.cpp likelihoodComputationGL.cpp \</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> threeStateModel.cpp threeStateAlphabet.cpp oneTwoMoreModel.cpp betaDistributionFixedCategories.cpp betaDistributionFixedCategoriesWithOmegaUniform.cpp \</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> bblEM2codon.cpp bestAlphaAndK.cpp fromCountTableComponentToDistance2Codon.cpp\</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> gtrModel.cpp bestGtrModelParams.cpp simulateRateShiftJumps.cpp integerAlphabet.cpp</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"># do not use: fromInstructionFile.cpp, simulateSequnce.cpp split.save.cpp</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"># LibCsources= cmdline.c</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"># LibCsources += getopt.c getopt1.c </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">EXEC = </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">#TEST_EXEC_SUB = split_test splitMap_test bootstrap_test</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">TEST_EXEC = $(addprefix tests/,$(TEST_EXEC_SUB))</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">LIB = libEvolTree.a</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">DEBUGLIB = $(LIB:.a=Debug.a)</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">DOUBLEREPLIB = $(LIB:.a=DoubleRep.a)</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">#CC=g++</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">CXX=g++</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">CC=$(CXX)</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">#requres 2.13, but may work with 2.11</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">GENGETOPT = gengetopt</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"># osX/tiger</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">#GENGETOPT = /opt/local/bin/gengetopt</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.SECONDARY: semphy_cmdline.c semphy_cmdline.h</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">#LDFLAGS= </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">CPPFLAGS= -O3 -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32AGSDEBUG= -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32 -DVERBOS</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">#CPPFLAGSDOU= $(CPPFLAGS) </span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">#-pg</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">#CPPFLAGS+= -I/usr/include/g++-v3</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">#CPPFLAGS+= -DLOG -DLOGCLS -DMEMCHK</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"># sources</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">sources= $(Libsources) $(LibCsources) $(addsuffix .cpp,$(EXEC) $(TEST_EXEC))</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.PHONY: tests lib test debug %.debug</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.PHONY: dat DOUBLEREP doubleRep</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">all: lib $(EXEC)</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">test: all tests</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> +cd tests; make -k test</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">#ifdef DOUBLEREP</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">#CPPFLAGS+= -DLOGREP</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">#CPPFLAGSDEBUG += -DLOGREP</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">#LDFLAGSDEBUG += -DLOGREP</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">#endif</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">ifdef DOUBLEREP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">CPPFLAGS+= -DDOUBLEREP</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">CPPFLAGSDEBUG += -DDOUBLEREP</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">LDFLAGSDEBUG += -DDOUBLEREP</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">endif</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-32</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">debug: $(DEBUGLIB)</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">pl:</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> @echo "lib ="$(LIB)</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> @echo "debug="$(DEBUGLIB)</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">#debug: all </span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"># cp libEvolTree.a libEvolTreeDebug.a</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"># <<<<<<< Makefile</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"># %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG -ftemplate-depth-25</span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"># % debug: LIB = libEvolTreeDebug.a</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"># %.debug: %</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"># @echo "made \""$(*)"\" in debug mode"</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"># =======</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">#>>>>>>> 2.34</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">lib: $(LIB)</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">$(LIB): $(Libsources:.cpp=.o) $(LibCsources:.c=.o)</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> ar rv $@ $?</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> ranlib $@</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">tags: *.cpp *.h</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> etags --members --language=c++ $^ </span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">$(EXEC) $(TEST_EXEC): $(LIB)</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">tests: $(TEST_EXEC)</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">-include make.dep</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">install:</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> cd ../fast; make -f Makefile.lib install_do</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">clean:</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> -rm -f $(LIB) $(DEBUGLIB) $(DOUBLEREPLIB) $(EXEC) $(TEST_EXEC) *.o</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">ifneq ($(wildcard make.dep), make.dep)</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> make.dep: depend</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">endif</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">depend makedep: _make.dep</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> @mv -f _make.dep make.dep </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">_make.dep: $(sources)</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> @echo making depend</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"># $(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed '\''s/\($*\)\.o[ :]*/\1.o $@ : /g'\'' > $@ ; [ -s $@ ] || rm -f $@' </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> @$(SHELL) -ec '$(CC) -MM $(CPPFLAGS) $^ | sed "s/\(^[^.]*\)\.o/\1.o \1.debug.o/g" > $@' </span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">_fast:</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> cd ../fast;make -f Makefile.lib -k all</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">fast.% _fast.%:</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> cd ../fast;make -f Makefile.lib -k $(*)</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">simulateSequnce: simulateSequnce_cmdline.o</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">evolObjsTest.ggo: evolObjs.header evolObjs.args</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> cat $^ > $@</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"># commandline (gengetopts)</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">%_cmdline.h %_cmdline.c: %.ggo</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> $(GENGETOPT) -i$< -F$(*)_cmdline</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">%.dat.q: %.dat</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> awk 'BEGIN{RS="[\n\r]+";};{print "\" "$$0" \"\r"}' $< > $@</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"># cat $@</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">DAT = cpREV45.dat.q dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">dat: $(DAT)</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">cleandat:</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> rm $(DAT)</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">datMatrixHolder.o: $(DAT)</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">.PRECIOUS: $(DAT)</span>
</pre>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"></span>
</pre>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">debug: LIB = $(DEBUGLIB)</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">%.debug: CPPFLAGS = $(CPPFLAGSDEBUG)</span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">%.debug: %</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> @echo "made \""$(*)"\" in debug mode"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"></span>
</pre>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"></span>
</pre>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">%.debug.o: %.c</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> $(CC) -c $(CPPFLAGSDEBUG) $(CFLAGS) $< -o $@</span>
</pre>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"></span>
</pre>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">%.debug.o: %.cpp</span>
</pre>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> $(CXX) -c $(CPPFLAGSDEBUG) $(CXXFLAGS) $< -o $@</span>
</pre>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"></span>
</pre>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">$(DEBUGLIB): $(Libsources:.cpp=.debug.o) $(LibCsources:.c=.debug.o)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> ar rv $@ $?</span>
</pre>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> ranlib $@</span>
</pre>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">#doubleRep: LOGREP=t</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">#doubleRep: CPPFLAGS+= -DLOGREP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">doubleRep: DOUBLEREP=t</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">doubleRep: CPPFLAGS+= -DDOUBLEREP</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">doubleRep: $(DOUBLEREPLIB)</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">%.doubleRep.o: %.c</span>
</pre>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> $(CC) -c $(CPPFLAGS) $(CFLAGS) $< -o $@</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">%.doubleRep.o: %.cpp</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> $(CXX) -c $(CPPFLAGS) $(CXXFLAGS) $< -o $@</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">$(DOUBLEREPLIB): $(Libsources:.cpp=.doubleRep.o) $(LibCsources:.c=.doubleRep.o)</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> ar rv $@ $?</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> ranlib $@</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"># DO NOT DELETE</span></pre>
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<li id="d0d2651a62d3379d9fd010fb694608d67975a0e6">
<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#d0d2651a62d3379d9fd010fb694608d67975a0e6"><strong>libs/phylogeny/Makefile</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,8 +88,8 @@ GENGETOPT = gengetopt</td>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#LDFLAGS= </span></span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-DLOG</span> <span class="nt" style="color: #000080;"><span class="idiff left right">-ftemplate-depth-32</span></span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGSDEBUG</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-DLOG</span> <span class="nt" style="color: #000080;">-<span class="idiff left">ftemplate-depth-32</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-</span>DVERBOS</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-DLOG</span> </span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGSDEBUG</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-DLOG</span> <span class="nt" style="color: #000080;">-DVERBOS</span></span>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#CPPFLAGSDOU= $(CPPFLAGS) </span></span>
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#-pg</span></span>
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="make"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -120,7 +120,7 @@ CPPFLAGSDEBUG += -DDOUBLEREP</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGSDEBUG</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-DDOUBLEREP</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="make"><span class="nl">debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG <span class="idiff left right">-ftemplate-depth-32</span></span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="make"><span class="nl">debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG </span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="make"><span class="nl">debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(DEBUGLIB)</span></span>
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125
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="make"><span class="nl">pl</span><span class="o" style="font-weight: 600;">:</span></span>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"lib ="</span><span class="nv" style="color: #008080;">$(LIB)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -129,7 +129,7 @@ pl:</td>
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># cp libEvolTree.a libEvolTreeDebug.a</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># <<<<<<< Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG <span class="idiff left right">-ftemplate-depth-25</span></span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># %.debug: CPPFLAGS = -g -Wall -Wno-sign-compare -I. -DLOG </span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># % debug: LIB = libEvolTreeDebug.a</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># %.debug: %</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># @echo "made \""$(*)"\" in debug mode"</span></span>
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<li id="f5773c791126ed6431e527cdccc7c8e5267e0db0">
<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#f5773c791126ed6431e527cdccc7c8e5267e0db0"><strong>libs/phylogeny/errorMsg.cpp</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// $Id: errorMsg.cpp <span class="idiff left right">6066 2009-04-14 19:11:10Z itayma</span>y $</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// $Id: errorMsg.cpp <span class="idiff left right">15479 2016-10-10 16:25:21Z elilev</span>y $</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// version 1.01</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// last modified 1 Jan 2004</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ void errorMsg::reportError(const vector<string>& textToPrint, const int exitCode</td>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">textToPrint</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">textToPrint</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">);</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">textToPrint</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_errorOut</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">_errorOut</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">cerr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_errorOut</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">_errorOut</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">&</span></span><span class="n" style="color: #333;">cerr</span><span class="p">)</span> <span class="p">{</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_errorOut</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">textToPrint</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ void errorMsg::reportError(const vector<string>& textToPrint, const int exitCode</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">errorMsg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reportError</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">textToPrint</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exitCode</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">LOG</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">textToPrint</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">);</span></span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">textToPrint</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_errorOut</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff">_errorOut</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">cerr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_errorOut</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">_errorOut</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">&</span></span><span class="n" style="color: #333;">cerr</span><span class="p">)</span> <span class="p">{</span></span>
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35
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">_errorOut</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">textToPrint</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="p">}</span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AddLog.o AddLog.debug.o: AddLog.cpp AddLog.h</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">NNiProp.o NNiProp.debug.o: NNiProp.cpp definitions.h treeIt.h errorMsg.h tree.h \</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> readTree.h logFile.h treeUtil.h NNiProp.h sequenceContainer.h sequence.h \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> bblEM.h countTableComponent.h computePijComponent.h \</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> generalGammaDistribution.h suffStatComponent.h unObservableData.h \</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> bblEMProportional.h</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">NNiSep.o NNiSep.debug.o: NNiSep.cpp definitions.h treeIt.h errorMsg.h tree.h readTree.h \</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> logFile.h treeUtil.h NNiSep.h sequenceContainer.h sequence.h alphabet.h \</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h bblEM.h \</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> unObservableData.h bblEMSeperate.h</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Nni.o Nni.debug.o: Nni.cpp definitions.h treeUtil.h tree.h readTree.h errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> logFile.h treeIt.h Nni.h sequenceContainer.h sequence.h alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h bblEM.h \</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> unObservableData.h</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">aaJC.o aaJC.debug.o: aaJC.cpp aaJC.h replacementModel.h definitions.h errorMsg.h</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">allTrees.o allTrees.debug.o: allTrees.cpp definitions.h allTrees.h tree.h readTree.h \</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> errorMsg.h logFile.h sequenceContainer.h sequence.h alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h treeUtil.h treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> bblEM.h countTableComponent.h computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> generalGammaDistribution.h suffStatComponent.h unObservableData.h</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">allTreesSeparateModel.o allTreesSeparateModel.debug.o: allTreesSeparateModel.cpp definitions.h treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> errorMsg.h tree.h readTree.h logFile.h allTreesSeparateModel.h \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> gainLossAlphabet.h stochasticProcess.h pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> replacementModel.h distribution.h bblEMSeperate.h</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">alphabet.o alphabet.debug.o: alphabet.cpp alphabet.h</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">amino.o amino.debug.o: amino.cpp amino.h definitions.h errorMsg.h alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> geneticCodeHolder.h codon.h someUtil.h logFile.h</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">bestAlpha.o bestAlpha.debug.o: bestAlpha.cpp bestAlpha.h definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> likelihoodComputation.h computePijComponent.h tree.h readTree.h \</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h bblEM.h countTableComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> bblEMProportionalEB.h bblLSProportionalEB.h numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> uniformDistribution.h</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">bestAlphaManyTrees.o bestAlphaManyTrees.debug.o: bestAlphaManyTrees.cpp bestAlphaManyTrees.h \</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> definitions.h computePijComponent.h tree.h readTree.h errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> distribution.h multipleStochasticProcess.h gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> generalGammaDistribution.h sequenceContainer.h sequence.h alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h bblEM.h \</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> countTableComponent.h suffStatComponent.h unObservableData.h \</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> likelihoodComputation.h bestAlpha.h numRec.h uniformDistribution.h \</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> bblEMProportional.h bblEMSeperate.h</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">bestHKYparam.o bestHKYparam.debug.o: bestHKYparam.cpp bestHKYparam.h definitions.h \</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> likelihoodComputation.h computePijComponent.h tree.h readTree.h \</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h hky.h bblEM.h \</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> numRec.h uniformDistribution.h bestAlpha.h</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">bootstrap.o bootstrap.debug.o: bootstrap.cpp definitions.h someUtil.h logFile.h alphabet.h \</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> bootstrap.h split.h splitMap.h tree.h readTree.h errorMsg.h treeUtil.h \</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> splitTreeUtil.h</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">bblEM.o bblEM.debug.o: bblEM.cpp bblEM.h definitions.h tree.h readTree.h errorMsg.h \</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> distribution.h sequenceContainer.h sequence.h alphabet.h mulAlphabet.h \</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> someUtil.h gainLossAlphabet.h countTableComponent.h \</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> generalGammaDistribution.h suffStatComponent.h unObservableData.h \</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> likelihoodComputation.h computeUpAlg.h computeDownAlg.h computeCounts.h \</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> treeIt.h fromCountTableComponentToDistance.h</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">bblEMfixRoot.o bblEMfixRoot.debug.o: bblEMfixRoot.cpp bblEMfixRoot.h definitions.h tree.h \</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> replacementModel.h distribution.h sequenceContainer.h sequence.h \</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> unObservableData.h likelihoodComputation.h computeUpAlg.h \</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> computeDownAlg.h computeCounts.h treeIt.h \</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> fromCountTableComponentToDistancefixRoot.h</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">bblEMProprtional.o bblEMProprtional.debug.o: bblEMProprtional.cpp bblEM.h definitions.h tree.h \</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> replacementModel.h distribution.h sequenceContainer.h sequence.h \</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> unObservableData.h bblEMProportional.h likelihoodComputation.h \</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> fromCountTableComponentToDistance.h \</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> fromCountTableComponentToDistanceProp.h</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">bblEMProportionalEB.o bblEMProportionalEB.debug.o: bblEMProportionalEB.cpp bblEM.h definitions.h \</span>
</pre>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
</pre>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
</pre>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> unObservableData.h bblEMProportionalEB.h likelihoodComputation.h \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \</span>
</pre>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> fromCountTableComponentToDistance.h \</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> fromCountTableComponentToDistancePropEB.h</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">bblLSProportionalEB.o bblLSProportionalEB.debug.o: bblLSProportionalEB.cpp bblLSProportionalEB.h \</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> definitions.h tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> generalGammaDistribution.h likelihoodComputation.h computePijComponent.h \</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h numRec.h uniformDistribution.h</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">bblEMSeperate.o bblEMSeperate.debug.o: bblEMSeperate.cpp bblEM.h definitions.h tree.h \</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> replacementModel.h distribution.h sequenceContainer.h sequence.h \</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> unObservableData.h bblEMSeperate.h</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">chebyshevAccelerator.o chebyshevAccelerator.debug.o: chebyshevAccelerator.cpp chebyshevAccelerator.h \</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> pijAccelerator.h definitions.h replacementModel.h</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">clustalFormat.o clustalFormat.debug.o: clustalFormat.cpp clustalFormat.h sequenceContainer.h \</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> logFile.h gainLossAlphabet.h codon.h geneticCodeHolder.h</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">codon.o codon.debug.o: codon.cpp codon.h definitions.h errorMsg.h someUtil.h logFile.h \</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> alphabet.h geneticCodeHolder.h nucleotide.h amino.h matrixUtils.h \</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> sequenceContainer.h sequence.h mulAlphabet.h gainLossAlphabet.h</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">codonJC.o codonJC.debug.o: codonJC.cpp codonJC.h replacementModel.h definitions.h</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">computeCounts.o computeCounts.debug.o: computeCounts.cpp computeCounts.h definitions.h \</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> countTableComponent.h sequenceContainer.h sequence.h errorMsg.h \</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h \</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> computePijComponent.h tree.h readTree.h stochasticProcess.h \</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h \</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> generalGammaDistribution.h suffStatComponent.h</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">computeDownAlg.o computeDownAlg.debug.o: computeDownAlg.cpp definitions.h computeDownAlg.h \</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> tree.h readTree.h errorMsg.h logFile.h suffStatComponent.h \</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> gainLossAlphabet.h computePijComponent.h stochasticProcess.h \</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h \</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> generalGammaDistribution.h treeIt.h</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">computeMarginalAlg.o computeMarginalAlg.debug.o: computeMarginalAlg.cpp definitions.h treeIt.h \</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> errorMsg.h tree.h readTree.h logFile.h computeMarginalAlg.h \</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> generalGammaDistribution.h</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">computePijComponent.o computePijComponent.debug.o: computePijComponent.cpp definitions.h treeIt.h \</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> errorMsg.h tree.h readTree.h logFile.h computePijComponent.h \</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> generalGammaDistribution.h</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">computeUpAlg.o computeUpAlg.debug.o: computeUpAlg.cpp definitions.h computeUpAlg.h tree.h \</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h suffStatComponent.h sequenceContainer.h \</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> computePijComponent.h stochasticProcess.h pijAccelerator.h \</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h treeIt.h \</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> seqContainerTreeMap.h</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">computeUpAlgFactors.o computeUpAlgFactors.debug.o: computeUpAlgFactors.cpp definitions.h \</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> computeUpAlg.h tree.h readTree.h errorMsg.h logFile.h \</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> generalGammaDistribution.h seqContainerTreeMap.h treeIt.h</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">computeSubstitutionCounts.o computeSubstitutionCounts.debug.o: computeSubstitutionCounts.cpp \</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> computeSubstitutionCounts.h definitions.h replacementModel.h \</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions.h simulateJumps.h \</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> simulateJumpsAbstract.h stochasticProcess.h pijAccelerator.h \</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> distribution.h suffStatComponent.h computePijComponent.h \</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> generalGammaDistribution.h \</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions_nonReversibleSp.h \</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> matrixUtils.h simulateCodonsJumps.h codon.h geneticCodeHolder.h treeIt.h \</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> treeUtil.h</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.debug.o: \</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions.cpp \</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions.h definitions.h \</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> simulateJumps.h simulateJumpsAbstract.h tree.h readTree.h errorMsg.h \</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> distribution.h alphabet.h sequenceContainer.h sequence.h mulAlphabet.h \</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> someUtil.h gainLossAlphabet.h suffStatComponent.h computePijComponent.h \</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> generalGammaDistribution.h computeDownAlg.h computeUpAlg.h matrixUtils.h \</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> treeIt.h likelihoodComputation.h unObservableData.h</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.debug.o: \</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp \</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> definitions.h computeDownAlg.h tree.h readTree.h errorMsg.h logFile.h \</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> generalGammaDistribution.h computeUpAlg.h matrixUtils.h treeIt.h \</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"> likelihoodComputation.h unObservableData.h \</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions_nonReversibleSp.h \</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"> computePosteriorExpectationOfSubstitutions.h simulateJumps.h \</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> simulateJumpsAbstract.h</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">ConversionUtils.o ConversionUtils.debug.o: ConversionUtils.cpp ConversionUtils.h definitions.h \</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> someUtil.h logFile.h alphabet.h errorMsg.h</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">countTableComponent.o countTableComponent.debug.o: countTableComponent.cpp countTableComponent.h \</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> definitions.h logFile.h</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">datMatrixHolder.o datMatrixHolder.debug.o: datMatrixHolder.cpp datMatrixHolder.h cpREV45.dat.q \</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> dayhoff.dat.q jones.dat.q mtREV24.dat.q wag.dat.q HIVb.dat.q HIVw.dat.q \</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> adrianCodon.dat.q LG.dat.q</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">distanceTable.o distanceTable.debug.o: distanceTable.cpp definitions.h distanceTable.h \</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> someUtil.h logFile.h sequenceContainer.h gainLossAlphabet.h</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">distribution.o distribution.debug.o: distribution.cpp distribution.h definitions.h errorMsg.h</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">errorMsg.o errorMsg.debug.o: errorMsg.cpp definitions.h errorMsg.h logFile.h</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">evaluateCharacterFreq.o evaluateCharacterFreq.debug.o: evaluateCharacterFreq.cpp \</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> evaluateCharacterFreq.h sequenceContainer.h definitions.h sequence.h \</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> gainLossAlphabet.h</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">fastStartTree.o fastStartTree.debug.o: fastStartTree.cpp definitions.h tree.h readTree.h \</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> errorMsg.h logFile.h treeUtil.h fastStartTree.h stochasticProcess.h \</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> bblEM.h countTableComponent.h computePijComponent.h \</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> generalGammaDistribution.h suffStatComponent.h unObservableData.h \</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> likeDist.h distanceMethod.h jcDistance.h likelihoodComputation.h \</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> getRandomWeights.h distanceTable.h nj.h njConstrain.h distances2Tree.h</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">fastaFormat.o fastaFormat.debug.o: fastaFormat.cpp fastaFormat.h sequenceContainer.h \</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> logFile.h gainLossAlphabet.h ConversionUtils.h</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">findRateOfGene.o findRateOfGene.debug.o: findRateOfGene.cpp definitions.h findRateOfGene.h \</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> numRec.h errorMsg.h uniformDistribution.h distribution.h logFile.h \</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> likelihoodComputation.h computePijComponent.h tree.h readTree.h \</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> generalGammaDistribution.h sequenceContainer.h sequence.h alphabet.h \</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h suffStatComponent.h \</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> unObservableData.h computeUpAlg.h</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">fromCountTableComponentToDistance.o fromCountTableComponentToDistance.debug.o: \</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> fromCountTableComponentToDistance.cpp \</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> fromCountTableComponentToDistance.h definitions.h countTableComponent.h \</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> unObservableData.h tree.h readTree.h errorMsg.h logFile.h \</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h likeDist.h \</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> distanceMethod.h jcDistance.h</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.debug.o: \</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> fromCountTableComponentToDistancefixRoot.cpp \</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"> fromCountTableComponentToDistancefixRoot.h definitions.h \</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> countTableComponent.h stochasticProcess.h pijAccelerator.h \</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> replacementModel.h distribution.h unObservableData.h tree.h readTree.h \</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> errorMsg.h logFile.h sequenceContainer.h sequence.h alphabet.h \</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> generalGammaDistribution.h likeDistfixRoot.h distanceMethod.h \</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> jcDistance.h</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.debug.o: \</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> fromCountTableComponentToDistanceProp.cpp \</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> fromCountTableComponentToDistanceProp.h definitions.h \</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> countTableComponent.h stochasticProcess.h pijAccelerator.h \</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> replacementModel.h distribution.h likeDistProp.h</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.debug.o: \</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> fromCountTableComponentToDistancePropEB.cpp \</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> fromCountTableComponentToDistancePropEB.h definitions.h \</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> countTableComponent.h multipleStochasticProcess.h stochasticProcess.h \</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> generalGammaDistribution.h errorMsg.h likeDistPropEB.h logFile.h</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">fromQtoPt.o fromQtoPt.debug.o: fromQtoPt.cpp definitions.h fromQtoPt.h replacementModel.h \</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> errorMsg.h numRec.h uniformDistribution.h distribution.h logFile.h \</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> matrixUtils.h</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.debug.o: \</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> generalGammaDistributionFixedCategories.cpp \</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> generalGammaDistributionFixedCategories.h definitions.h \</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> generalGammaDistribution.h distribution.h errorMsg.h gammaUtilities.h \</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> numRec.h uniformDistribution.h logFile.h</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">gammaDistribution.o gammaDistribution.debug.o: gammaDistribution.cpp definitions.h \</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h distribution.h errorMsg.h \</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"> gammaUtilities.h numRec.h uniformDistribution.h logFile.h</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">gammaUtilities.o gammaUtilities.debug.o: gammaUtilities.cpp gammaUtilities.h definitions.h \</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext"> numRec.h errorMsg.h uniformDistribution.h distribution.h logFile.h</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">generalGammaDistribution.o generalGammaDistribution.debug.o: generalGammaDistribution.cpp \</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"> generalGammaDistribution.h definitions.h distribution.h gammaUtilities.h \</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"> numRec.h errorMsg.h uniformDistribution.h logFile.h</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">getRandomWeights.o getRandomWeights.debug.o: getRandomWeights.cpp getRandomWeights.h definitions.h \</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"> talRandom.h logFile.h</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">goldmanYangModel.o goldmanYangModel.debug.o: goldmanYangModel.cpp goldmanYangModel.h definitions.h \</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> replacementModel.h fromQtoPt.h granthamChemicalDistances.h codon.h \</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"> errorMsg.h someUtil.h logFile.h alphabet.h geneticCodeHolder.h \</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> readDatMatrix.h datMatrixHolder.h</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">granthamChemicalDistances.o granthamChemicalDistances.debug.o: granthamChemicalDistances.cpp \</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext"> granthamChemicalDistances.h definitions.h</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">hky.o hky.debug.o: hky.cpp hky.h replacementModel.h definitions.h errorMsg.h</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">simulateWithDependence.o simulateWithDependence.debug.o: simulateWithDependence.cpp \</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> simulateWithDependence.h tree.h definitions.h readTree.h errorMsg.h \</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> logFile.h alphabet.h nucleotide.h simulateTree.h stochasticProcess.h \</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> sequence.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> trivialAccelerator.h uniDistribution.h \</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> generalGammaDistributionPlusInvariant.h distributionPlusInvariant.h \</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> generalGammaDistribution.h gammaUtilities.h numRec.h \</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> uniformDistribution.h fastaFormat.h gtrModel.h fromQtoPt.h</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">KH_calculation.o KH_calculation.debug.o: KH_calculation.cpp KH_calculation.h definitions.h</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">likeDist.o likeDist.debug.o: likeDist.cpp likeDist.h definitions.h countTableComponent.h \</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> replacementModel.h distribution.h jcDistance.h unObservableData.h tree.h \</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"> readTree.h sequenceContainer.h gainLossAlphabet.h computePijComponent.h \</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> generalGammaDistribution.h numRec.h uniformDistribution.h</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">likeDistfixRoot.o likeDistfixRoot.debug.o: likeDistfixRoot.cpp likeDistfixRoot.h definitions.h \</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> replacementModel.h distribution.h jcDistance.h sequenceContainer.h \</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> gainLossAlphabet.h unObservableData.h tree.h readTree.h \</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> generalGammaDistribution.h numRec.h uniformDistribution.h</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">likeDistProp.o likeDistProp.debug.o: likeDistProp.cpp likeDistProp.h definitions.h \</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> countTableComponent.h stochasticProcess.h pijAccelerator.h \</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"> replacementModel.h distribution.h numRec.h errorMsg.h \</span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> uniformDistribution.h logFile.h</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">likeDistPropEB.o likeDistPropEB.debug.o: likeDistPropEB.cpp likeDistPropEB.h definitions.h \</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> countTableComponent.h multipleStochasticProcess.h stochasticProcess.h \</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"> generalGammaDistribution.h errorMsg.h logFile.h numRec.h \</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> uniformDistribution.h</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">likelihoodComputation.o likelihoodComputation.debug.o: likelihoodComputation.cpp definitions.h tree.h \</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h computeUpAlg.h suffStatComponent.h \</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext"> sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> gainLossAlphabet.h computePijComponent.h stochasticProcess.h \</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h \</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"> generalGammaDistribution.h likelihoodComputation.h unObservableData.h \</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"> gammaUtilities.h numRec.h uniformDistribution.h</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">likelihoodComputationFactors.o likelihoodComputationFactors.debug.o: likelihoodComputationFactors.cpp \</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"> definitions.h tree.h readTree.h errorMsg.h logFile.h computeUpAlg.h \</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"> suffStatComponent.h sequenceContainer.h sequence.h alphabet.h \</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> mulAlphabet.h someUtil.h gainLossAlphabet.h computePijComponent.h \</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"> generalGammaDistribution.h likelihoodComputationFactors.h</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">logFile.o logFile.debug.o: logFile.cpp logFile.h errorMsg.h</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">maseFormat.o maseFormat.debug.o: maseFormat.cpp maseFormat.h sequenceContainer.h \</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext"> definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext"> logFile.h gainLossAlphabet.h</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">molphyFormat.o molphyFormat.debug.o: molphyFormat.cpp molphyFormat.h sequenceContainer.h \</span>
</pre>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"> definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext"> logFile.h gainLossAlphabet.h</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">nexusFormat.o nexusFormat.debug.o: nexusFormat.cpp nexusFormat.h sequenceContainer.h \</span>
</pre>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext"> definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \</span>
</pre>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> logFile.h gainLossAlphabet.h</span>
</pre>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">nj.o nj.debug.o: nj.cpp nj.h definitions.h tree.h readTree.h errorMsg.h logFile.h \</span>
</pre>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext"> sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \</span>
</pre>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext"> gainLossAlphabet.h njConstrain.h distances2Tree.h treeUtil.h</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">njConstrain.o njConstrain.debug.o: njConstrain.cpp definitions.h njConstrain.h \</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"> sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext"> someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">nucJC.o nucJC.debug.o: nucJC.cpp nucJC.h replacementModel.h definitions.h</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">nucleotide.o nucleotide.debug.o: nucleotide.cpp nucleotide.h definitions.h alphabet.h \</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext"> errorMsg.h</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">numRec.o numRec.debug.o: numRec.cpp numRec.h definitions.h errorMsg.h \</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext"> uniformDistribution.h distribution.h logFile.h matrixUtils.h</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">Parameters.o Parameters.debug.o: Parameters.cpp Parameters.h ConversionUtils.h definitions.h</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">phylipFormat.o phylipFormat.debug.o: phylipFormat.cpp phylipFormat.h definitions.h \</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext"> sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext"> someUtil.h logFile.h gainLossAlphabet.h</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">pijAccelerator.o pijAccelerator.debug.o: pijAccelerator.cpp pijAccelerator.h definitions.h \</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext"> replacementModel.h</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">readDatMatrix.o readDatMatrix.debug.o: readDatMatrix.cpp readDatMatrix.h definitions.h \</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext"> datMatrixHolder.h replacementModel.h errorMsg.h logFile.h fromQtoPt.h</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">readTree.o readTree.debug.o: readTree.cpp definitions.h errorMsg.h someUtil.h logFile.h \</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext"> alphabet.h readTree.h</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">recognizeFormat.o recognizeFormat.debug.o: recognizeFormat.cpp recognizeFormat.h \</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext"> sequenceContainer.h definitions.h sequence.h errorMsg.h alphabet.h \</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h maseFormat.h \</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext"> molphyFormat.h phylipFormat.h nexusFormat.h fastaFormat.h \</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext"> clustalFormat.h phylipSequentialFormat.h</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">replacementModel.o replacementModel.debug.o: replacementModel.cpp replacementModel.h definitions.h</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">searchStatus.o searchStatus.debug.o: searchStatus.cpp searchStatus.h definitions.h</span>
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<td class="diff-line-num new new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">seqContainerTreeMap.o seqContainerTreeMap.debug.o: seqContainerTreeMap.cpp seqContainerTreeMap.h \</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext"> definitions.h tree.h readTree.h errorMsg.h logFile.h treeIt.h \</span>
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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext"> sequenceContainer.h sequence.h alphabet.h mulAlphabet.h someUtil.h \</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"> gainLossAlphabet.h treeUtil.h</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">sequence.o sequence.debug.o: sequence.cpp sequence.h definitions.h errorMsg.h alphabet.h \</span>
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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h</span>
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<td class="diff-line-num new new_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">sequenceContainer.o sequenceContainer.debug.o: sequenceContainer.cpp sequenceContainer.h \</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext"> definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext"> logFile.h gainLossAlphabet.h fastaFormat.h</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">simulateTree.o simulateTree.debug.o: simulateTree.cpp definitions.h treeUtil.h tree.h \</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h simulateTree.h stochasticProcess.h \</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext"> talRandom.h gammaDistribution.h generalGammaDistribution.h codon.h \</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext"> geneticCodeHolder.h</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext">siteSpecificRate.o siteSpecificRate.debug.o: siteSpecificRate.cpp siteSpecificRate.h definitions.h \</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext"> tree.h readTree.h errorMsg.h logFile.h sequenceContainer.h sequence.h \</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"> multipleStochasticProcess.h computePijComponent.h gammaDistribution.h \</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"> generalGammaDistribution.h unObservableData.h numRec.h \</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext"> uniformDistribution.h checkcovFanctors.h likelihoodComputation.h \</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> suffStatComponent.h</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext">someUtil.o someUtil.debug.o: someUtil.cpp someUtil.h logFile.h definitions.h alphabet.h \</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext"> errorMsg.h talRandom.h</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">split.o split.debug.o: split.cpp split.h definitions.h</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext">splitMap.o splitMap.debug.o: splitMap.cpp splitMap.h definitions.h split.h</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext">splitTreeUtil.o splitTreeUtil.debug.o: splitTreeUtil.cpp splitTreeUtil.h tree.h definitions.h \</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h split.h someUtil.h alphabet.h</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">stochasticProcess.o stochasticProcess.debug.o: stochasticProcess.cpp stochasticProcess.h \</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext"> pijAccelerator.h definitions.h replacementModel.h distribution.h \</span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext"> errorMsg.h</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext">suffStatComponent.o suffStatComponent.debug.o: suffStatComponent.cpp suffStatComponent.h \</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext"> definitions.h</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext">talRandom.o talRandom.debug.o: talRandom.cpp talRandom.h definitions.h logFile.h</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">tree.o tree.debug.o: tree.cpp definitions.h tree.h readTree.h errorMsg.h logFile.h \</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> treeUtil.h someUtil.h alphabet.h</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">treeIt.o treeIt.debug.o: treeIt.cpp definitions.h treeIt.h errorMsg.h tree.h readTree.h \</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext"> logFile.h</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext">treeUtil.o treeUtil.debug.o: treeUtil.cpp definitions.h treeUtil.h tree.h readTree.h \</span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext"> errorMsg.h logFile.h treeIt.h someUtil.h alphabet.h</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">uniDistribution.o uniDistribution.debug.o: uniDistribution.cpp uniDistribution.h distribution.h \</span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext"> definitions.h errorMsg.h</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext">uniformDistribution.o uniformDistribution.debug.o: uniformDistribution.cpp uniformDistribution.h \</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"> definitions.h distribution.h</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext">cmdline2EvolObjs.o cmdline2EvolObjs.debug.o: cmdline2EvolObjs.cpp cmdline2EvolObjs.h amino.h \</span>
</pre>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext"> definitions.h errorMsg.h alphabet.h geneticCodeHolder.h codon.h \</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext"> someUtil.h logFile.h nucleotide.h sequenceContainer.h sequence.h \</span>
</pre>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext"> mulAlphabet.h gainLossAlphabet.h tree.h readTree.h stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h uniDistribution.h \</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext"> trivialAccelerator.h alphaTrivialAccelerator.h readDatMatrix.h \</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext"> datMatrixHolder.h chebyshevAccelerator.h talRandom.h nucJC.h aaJC.h \</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext"> hky.h tamura92.h gtrModel.h fromQtoPt.h gammaDistribution.h \</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext"> generalGammaDistribution.h recognizeFormat.h replacementModelSSRV.h \</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext"> stochasticProcessSSRV.h</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext">generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.debug.o: generalGammaDistributionLaguerre.cpp \</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext"> generalGammaDistributionLaguerre.h definitions.h \</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext"> generalGammaDistribution.h distribution.h gammaUtilities.h numRec.h \</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext"> errorMsg.h uniformDistribution.h logFile.h GLaguer.h</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">gammaDistributionLaguerre.o gammaDistributionLaguerre.debug.o: gammaDistributionLaguerre.cpp \</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext"> gammaDistributionLaguerre.h definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext"> generalGammaDistributionLaguerre.h generalGammaDistribution.h \</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext"> distribution.h errorMsg.h gammaUtilities.h numRec.h \</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext"> uniformDistribution.h logFile.h</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext">GLaguer.o GLaguer.debug.o: GLaguer.cpp definitions.h GLaguer.h errorMsg.h \</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"> gammaUtilities.h numRec.h uniformDistribution.h distribution.h logFile.h</span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext">givenRatesMLDistance.o givenRatesMLDistance.debug.o: givenRatesMLDistance.cpp givenRatesMLDistance.h \</span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext"> definitions.h countTableComponent.h likeDist.h distanceMethod.h \</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext"> sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext"> jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext"> gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h numRec.h \</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext"> uniformDistribution.h</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.debug.o: distanceBasedSeqs2Tree.cpp \</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext"> distanceBasedSeqs2Tree.h distanceMethod.h definitions.h sequence.h \</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext"> errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext"> sequenceContainer.h gainLossAlphabet.h stochasticProcess.h \</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h likeDist.h \</span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext"> countTableComponent.h jcDistance.h unObservableData.h tree.h readTree.h \</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext"> computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext"> generalGammaDistribution.h distances2Tree.h givenRatesMLDistance.h \</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext"> posteriorDistance.h uniDistribution.h distanceTable.h bestAlpha.h \</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext"> likelihoodComputation.h suffStatComponent.h siteSpecificRate.h bblEM.h \</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext"> tamura92.h bestTamura92param.h bestGtrModelParams.h gtrModel.h \</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext"> fromQtoPt.h replacementModelSSRV.h trivialAccelerator.h</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext">posteriorDistance.o posteriorDistance.debug.o: posteriorDistance.cpp posteriorDistance.h likeDist.h \</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext"> definitions.h countTableComponent.h distanceMethod.h sequence.h \</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext"> errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h replacementModel.h distribution.h \</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext"> jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext"> gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \</span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h numRec.h \</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext"> uniformDistribution.h uniDistribution.h</span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext">pairwiseGammaDistance.o pairwiseGammaDistance.debug.o: pairwiseGammaDistance.cpp \</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext"> pairwiseGammaDistance.h likeDist.h definitions.h countTableComponent.h \</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext"> distanceMethod.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
</pre>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"> someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"> replacementModel.h distribution.h jcDistance.h unObservableData.h tree.h \</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"> readTree.h sequenceContainer.h gainLossAlphabet.h computePijComponent.h \</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h \</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> generalGammaDistribution.h numRec.h uniformDistribution.h \</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext"> uniDistribution.h</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">doubleRep.o doubleRep.debug.o: doubleRep.cpp</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">logRep.o logRep.debug.o: logRep.cpp</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext">indel.o indel.debug.o: indel.cpp indel.h definitions.h errorMsg.h alphabet.h</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext">indelModel.o indelModel.debug.o: indelModel.cpp indelModel.h replacementModel.h \</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext"> definitions.h</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext">mulAlphabet.o mulAlphabet.debug.o: mulAlphabet.cpp mulAlphabet.h definitions.h alphabet.h \</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext"> someUtil.h logFile.h distribution.h errorMsg.h</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext">replacementModelSSRV.o replacementModelSSRV.debug.o: replacementModelSSRV.cpp replacementModelSSRV.h \</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext"> replacementModel.h definitions.h distribution.h fromQtoPt.h errorMsg.h \</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext"> logFile.h</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext">stochasticProcessSSRV.o stochasticProcessSSRV.debug.o: stochasticProcessSSRV.cpp \</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"> stochasticProcessSSRV.h stochasticProcess.h pijAccelerator.h \</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext"> definitions.h replacementModel.h distribution.h replacementModelSSRV.h \</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext"> fromQtoPt.h errorMsg.h</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext">bestAlphaAndNu.o bestAlphaAndNu.debug.o: bestAlphaAndNu.cpp bestAlphaAndNu.h definitions.h \</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"> sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"> someUtil.h logFile.h gainLossAlphabet.h stochasticProcess.h \</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> generalGammaDistribution.h tree.h readTree.h replacementModelSSRV.h \</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> fromQtoPt.h tamura92.h stochasticProcessSSRV.h C_evalParamUSSRV.h \</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> likelihoodComputation.h computePijComponent.h \</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext"> multipleStochasticProcess.h suffStatComponent.h unObservableData.h \</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext"> likelihoodComputation2USSRV.h ussrvModel.h computeUpAlg.h bestAlpha.h \</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext"> numRec.h uniformDistribution.h bblEM.h countTableComponent.h</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext">C_evalParamUSSRV.o C_evalParamUSSRV.debug.o: C_evalParamUSSRV.cpp C_evalParamUSSRV.h definitions.h \</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext"> likelihoodComputation.h computePijComponent.h tree.h readTree.h \</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext"> errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h likelihoodComputation2USSRV.h \</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext"> ussrvModel.h stochasticProcessSSRV.h replacementModelSSRV.h fromQtoPt.h \</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext"> computeUpAlg.h tamura92.h</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext">matrixUtils.o matrixUtils.debug.o: matrixUtils.cpp matrixUtils.h definitions.h logFile.h \</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext"> errorMsg.h</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext">betaOmegaDistribution.o betaOmegaDistribution.debug.o: betaOmegaDistribution.cpp \</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext"> betaOmegaDistribution.h definitions.h distribution.h betaDistribution.h \</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext"> logFile.h gammaUtilities.h numRec.h errorMsg.h uniformDistribution.h \</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"> betaUtilities.h</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext">betaUtilities.o betaUtilities.debug.o: betaUtilities.cpp definitions.h betaUtilities.h numRec.h \</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"> errorMsg.h uniformDistribution.h distribution.h logFile.h \</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext"> gammaUtilities.h</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext">betaDistribution.o betaDistribution.debug.o: betaDistribution.cpp betaDistribution.h definitions.h \</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext"> distribution.h gammaUtilities.h numRec.h errorMsg.h \</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> uniformDistribution.h logFile.h betaUtilities.h</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext">geneticCodeHolder.o geneticCodeHolder.debug.o: geneticCodeHolder.cpp geneticCodeHolder.h \</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"> replacementMatrixSource/nuclearStandard.code \</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext"> replacementMatrixSource/nuclearEuplotid.code \</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"> replacementMatrixSource/nuclearCiliate.code \</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext"> replacementMatrixSource/nuclearBlepharisma.code \</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"> replacementMatrixSource/mitochondriaYeast.code \</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext"> replacementMatrixSource/mitochondriaVertebrate.code \</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext"> replacementMatrixSource/mitochondriaProtozoan.code \</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext"> replacementMatrixSource/mitochondriaInvertebrate.code \</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext"> replacementMatrixSource/mitochondriaFlatworm.code \</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext"> replacementMatrixSource/mitochondriaEchinoderm.code \</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext"> replacementMatrixSource/mitochondriaAscidian.code</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext">samplingSequences.o samplingSequences.debug.o: samplingSequences.cpp samplingSequences.h \</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext"> definitions.h distanceMethod.h sequence.h errorMsg.h alphabet.h \</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h sequenceContainer.h \</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext"> gainLossAlphabet.h pDistance.h talRandom.h</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext">bblEM2USSRV.o bblEM2USSRV.debug.o: bblEM2USSRV.cpp bblEM2USSRV.h definitions.h tree.h \</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext"> replacementModel.h distribution.h sequenceContainer.h sequence.h \</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext"> ussrvModel.h stochasticProcessSSRV.h replacementModelSSRV.h fromQtoPt.h \</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext"> computeUpAlg.h computeDownAlg.h computeCounts.h treeIt.h \</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext"> fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h \</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext"> distanceMethod.h likelihoodComputation2USSRV.h likelihoodComputation.h \</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext"> unObservableData.h</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext">bestParamUSSRV.o bestParamUSSRV.debug.o: bestParamUSSRV.cpp bestParamUSSRV.h definitions.h \</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext"> sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext"> someUtil.h logFile.h gainLossAlphabet.h stochasticProcess.h \</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h gammaDistribution.h \</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext"> generalGammaDistribution.h tree.h readTree.h replacementModelSSRV.h \</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext"> fromQtoPt.h stochasticProcessSSRV.h C_evalParamUSSRV.h \</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext"> likelihoodComputation.h computePijComponent.h \</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext"> multipleStochasticProcess.h suffStatComponent.h unObservableData.h \</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext"> likelihoodComputation2USSRV.h ussrvModel.h computeUpAlg.h tamura92.h \</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext"> bestAlpha.h numRec.h uniformDistribution.h bblEM.h countTableComponent.h \</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="plaintext"> bestAlphaAndNu.h bblEM2USSRV.h computeDownAlg.h computeCounts.h treeIt.h \</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="plaintext"> fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h \</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext"> distanceMethod.h</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext">likeDist2USSRV.o likeDist2USSRV.debug.o: likeDist2USSRV.cpp likeDist2USSRV.h definitions.h \</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext"> countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext"> replacementModel.h distribution.h ussrvModel.h stochasticProcessSSRV.h \</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext"> replacementModelSSRV.h fromQtoPt.h gammaDistribution.h \</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext"> generalGammaDistribution.h numRec.h uniformDistribution.h</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext">ussrvModel.o ussrvModel.debug.o: ussrvModel.cpp ussrvModel.h stochasticProcessSSRV.h \</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext"> stochasticProcess.h pijAccelerator.h definitions.h replacementModel.h \</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext"> distribution.h replacementModelSSRV.h fromQtoPt.h errorMsg.h \</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h logFile.h</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext">likelihoodComputation2USSRV.o likelihoodComputation2USSRV.debug.o: likelihoodComputation2USSRV.cpp \</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> likelihoodComputation2USSRV.h definitions.h computePijComponent.h tree.h \</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="plaintext"> suffStatComponent.h ussrvModel.h stochasticProcessSSRV.h \</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext"> replacementModelSSRV.h fromQtoPt.h computeUpAlg.h \</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext"> likelihoodComputation.h unObservableData.h</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext">fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.debug.o: \</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="plaintext"> fromCountTableComponentToDistance2USSRV.cpp \</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext"> fromCountTableComponentToDistance2USSRV.h definitions.h \</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="plaintext"> countTableComponent.h stochasticProcess.h pijAccelerator.h \</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext"> replacementModel.h distribution.h ussrvModel.h stochasticProcessSSRV.h \</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext"> replacementModelSSRV.h fromQtoPt.h errorMsg.h gammaDistribution.h \</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext"> generalGammaDistribution.h logFile.h likeDist2USSRV.h distanceMethod.h \</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h likeDist.h jcDistance.h \</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext"> unObservableData.h tree.h readTree.h sequenceContainer.h \</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext"> gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext">normalDist.o normalDist.debug.o: normalDist.cpp normalDist.h definitions.h</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="plaintext">tamura92.o tamura92.debug.o: tamura92.cpp tamura92.h replacementModel.h definitions.h \</span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext"> errorMsg.h</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="plaintext">bestTamura92param.o bestTamura92param.debug.o: bestTamura92param.cpp bestTamura92param.h \</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext"> definitions.h likelihoodComputation.h computePijComponent.h tree.h \</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h tamura92.h bblEM.h \</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext"> countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext"> numRec.h uniformDistribution.h bestAlpha.h</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext">phylipSequentialFormat.o phylipSequentialFormat.debug.o: phylipSequentialFormat.cpp \</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext"> phylipSequentialFormat.h definitions.h sequenceContainer.h sequence.h \</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext"> errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext"> gainLossAlphabet.h</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext">simulateCodonsJumps.o simulateCodonsJumps.debug.o: simulateCodonsJumps.cpp simulateCodonsJumps.h \</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext"> simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext"> logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="plaintext"> distribution.h alphabet.h codon.h someUtil.h geneticCodeHolder.h \</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext"> talRandom.h</span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext">simulateJumpsAbstract.o simulateJumpsAbstract.debug.o: simulateJumpsAbstract.cpp \</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="plaintext"> simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext"> logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext"> distribution.h alphabet.h</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="plaintext">ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.debug.o: ssrvDistanceSeqs2Tree.cpp \</span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext"> ssrvDistanceSeqs2Tree.h distanceBasedSeqs2Tree.h distanceMethod.h \</span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="plaintext"> definitions.h sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h \</span>
</pre>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext"> logFile.h sequenceContainer.h gainLossAlphabet.h stochasticProcess.h \</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h likeDist.h \</span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext"> countTableComponent.h jcDistance.h unObservableData.h tree.h readTree.h \</span>
</pre>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="plaintext"> computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext"> generalGammaDistribution.h distances2Tree.h givenRatesMLDistance.h \</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext"> posteriorDistance.h bestParamUSSRV.h replacementModelSSRV.h fromQtoPt.h \</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext"> stochasticProcessSSRV.h C_evalParamUSSRV.h likelihoodComputation.h \</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext"> suffStatComponent.h likelihoodComputation2USSRV.h ussrvModel.h \</span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext"> computeUpAlg.h tamura92.h bestAlpha.h numRec.h uniformDistribution.h \</span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext"> bblEM.h bestAlphaAndNu.h bblEM2USSRV.h computeDownAlg.h computeCounts.h \</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext"> treeIt.h fromCountTableComponentToDistance2USSRV.h likeDist2USSRV.h</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="plaintext">multipleStochasticProcess.o multipleStochasticProcess.debug.o: multipleStochasticProcess.cpp \</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext"> multipleStochasticProcess.h stochasticProcess.h pijAccelerator.h \</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext"> definitions.h replacementModel.h distribution.h errorMsg.h</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext">distributionPlusInvariant.o distributionPlusInvariant.debug.o: distributionPlusInvariant.cpp definitions.h \</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext"> distributionPlusInvariant.h distribution.h errorMsg.h logFile.h</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">extremeValDistribution.o extremeValDistribution.debug.o: extremeValDistribution.cpp \</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext"> extremeValDistribution.h definitions.h</span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext">gammaDistributionFixedCategories.o gammaDistributionFixedCategories.debug.o: gammaDistributionFixedCategories.cpp \</span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext"> gammaDistributionFixedCategories.h definitions.h \</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext"> generalGammaDistributionFixedCategories.h generalGammaDistribution.h \</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext"> distribution.h errorMsg.h gammaUtilities.h numRec.h \</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext"> uniformDistribution.h logFile.h matrixUtils.h</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext">generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.debug.o: \</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext"> generalGammaDistributionPlusInvariant.cpp \</span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext"> generalGammaDistributionPlusInvariant.h definitions.h \</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext"> distributionPlusInvariant.h distribution.h generalGammaDistribution.h \</span>
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653
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext"> errorMsg.h gammaUtilities.h numRec.h uniformDistribution.h logFile.h</span>
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654
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="plaintext">gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.debug.o: gammaDistributionPlusInvariant.cpp \</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="plaintext"> gammaDistributionPlusInvariant.h definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="plaintext"> distributionPlusInvariant.h distribution.h gammaDistribution.h \</span>
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657
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext"> generalGammaDistribution.h errorMsg.h gammaUtilities.h numRec.h \</span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext"> uniformDistribution.h logFile.h</span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext">distributionPlusCategory.o distributionPlusCategory.debug.o: distributionPlusCategory.cpp \</span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext"> distributionPlusCategory.h definitions.h distribution.h logFile.h \</span>
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661
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext"> errorMsg.h</span>
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662
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext">simulateJumps.o simulateJumps.debug.o: simulateJumps.cpp simulateJumps.h \</span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext"> simulateJumpsAbstract.h definitions.h tree.h readTree.h errorMsg.h \</span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext"> logFile.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext"> distribution.h alphabet.h talRandom.h someUtil.h</span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext">computeJumps.o computeJumps.debug.o: computeJumps.cpp computeJumps.h definitions.h tree.h \</span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext"> replacementModel.h distribution.h alphabet.h someUtil.h talRandom.h \</span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext"> matrixUtils.h</span>
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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext">seqeuncesFilter.o seqeuncesFilter.debug.o: seqeuncesFilter.cpp seqeuncesFilter.h definitions.h \</span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext"> sequenceContainer.h sequence.h errorMsg.h alphabet.h mulAlphabet.h \</span>
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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext"> someUtil.h logFile.h gainLossAlphabet.h codon.h geneticCodeHolder.h \</span>
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673
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext"> amino.h fastaFormat.h nucleotide.h</span>
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674
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext">optGammaMixtureLS.o optGammaMixtureLS.debug.o: optGammaMixtureLS.cpp optGammaMixtureLS.h \</span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext"> definitions.h suffStatGammaMixture.h stochasticProcess.h \</span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext"> sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext"> gainLossAlphabet.h tree.h readTree.h mixtureDistribution.h \</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext"> generalGammaDistribution.h computePijComponent.h \</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h gammaUtilities.h \</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext"> numRec.h uniformDistribution.h likelihoodComputation.h \</span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext">mixtureDistribution.o mixtureDistribution.debug.o: mixtureDistribution.cpp mixtureDistribution.h \</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext"> definitions.h generalGammaDistribution.h distribution.h \</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext"> generalGammaDistributionLaguerre.h talRandom.h logFile.h someUtil.h \</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="plaintext"> alphabet.h errorMsg.h</span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="plaintext">suffStatGammaMixture.o suffStatGammaMixture.debug.o: suffStatGammaMixture.cpp suffStatGammaMixture.h \</span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="plaintext"> definitions.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="plaintext"> distribution.h sequenceContainer.h sequence.h errorMsg.h alphabet.h \</span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="plaintext"> mixtureDistribution.h generalGammaDistribution.h computePijComponent.h \</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h likelihoodComputation.h \</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h gammaUtilities.h numRec.h \</span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="plaintext"> uniformDistribution.h uniDistribution.h</span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="plaintext">GamMixtureOptimizer.o GamMixtureOptimizer.debug.o: GamMixtureOptimizer.cpp GamMixtureOptimizer.h \</span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="plaintext"> definitions.h stochasticProcess.h pijAccelerator.h replacementModel.h \</span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="plaintext"> distribution.h sequenceContainer.h sequence.h errorMsg.h alphabet.h \</span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h gainLossAlphabet.h tree.h readTree.h \</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="plaintext"> mixtureDistribution.h generalGammaDistribution.h unObservableData.h \</span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="plaintext"> computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \</span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="plaintext"> optGammaMixtureEM.h suffStatGammaMixture.h gammaUtilities.h numRec.h \</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="plaintext"> uniformDistribution.h optGammaMixtureLS.h likelihoodComputation.h \</span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="plaintext"> suffStatComponent.h</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="plaintext">optGammaMixtureEM.o optGammaMixtureEM.debug.o: optGammaMixtureEM.cpp optGammaMixtureEM.h \</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="plaintext"> definitions.h suffStatGammaMixture.h stochasticProcess.h \</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="plaintext"> sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="plaintext"> gainLossAlphabet.h tree.h readTree.h mixtureDistribution.h \</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="plaintext"> generalGammaDistribution.h computePijComponent.h \</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext"> multipleStochasticProcess.h gammaDistribution.h gammaUtilities.h \</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="plaintext"> numRec.h uniformDistribution.h likelihoodComputation.h \</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h uniDistribution.h</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="plaintext">gainLossAlphabet.o gainLossAlphabet.debug.o: gainLossAlphabet.cpp gainLossAlphabet.h alphabet.h \</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="plaintext"> errorMsg.h</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext">wYangModel.o wYangModel.debug.o: wYangModel.cpp wYangModel.h replacementModel.h \</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="plaintext"> definitions.h fromQtoPt.h codon.h errorMsg.h someUtil.h logFile.h \</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="plaintext"> alphabet.h geneticCodeHolder.h readDatMatrix.h datMatrixHolder.h</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="plaintext">codonUtils.o codonUtils.debug.o: codonUtils.cpp codonUtils.h nucleotide.h definitions.h \</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="plaintext"> alphabet.h codon.h errorMsg.h someUtil.h logFile.h geneticCodeHolder.h \</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="plaintext"> amino.h fastaFormat.h sequenceContainer.h sequence.h mulAlphabet.h \</span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="plaintext"> gainLossAlphabet.h clustalFormat.h recognizeFormat.h stochasticProcess.h \</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h wYangModel.h \</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="plaintext"> fromQtoPt.h evaluateCharacterFreq.h numRec.h uniformDistribution.h</span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="plaintext">likelihoodComputation2Codon.o likelihoodComputation2Codon.debug.o: likelihoodComputation2Codon.cpp \</span>
</pre>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="plaintext"> likelihoodComputation2Codon.h definitions.h computePijComponent.h tree.h \</span>
</pre>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
</pre>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
</pre>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="plaintext"> suffStatComponent.h wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h \</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="plaintext"> computeUpAlg.h likelihoodComputation.h unObservableData.h</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="plaintext">likeDist2Codon.o likeDist2Codon.debug.o: likeDist2Codon.cpp likeDist2Codon.h definitions.h \</span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="plaintext"> countTableComponent.h distanceMethod.h sequence.h errorMsg.h alphabet.h \</span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="plaintext"> mulAlphabet.h someUtil.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="plaintext"> replacementModel.h distribution.h wYangModel.h fromQtoPt.h codon.h \</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="plaintext"> geneticCodeHolder.h numRec.h uniformDistribution.h</span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="plaintext">unObservableData.o unObservableData.debug.o: unObservableData.cpp unObservableData.h definitions.h \</span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="plaintext"> tree.h readTree.h errorMsg.h logFile.h stochasticProcess.h \</span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="plaintext"> pijAccelerator.h replacementModel.h distribution.h sequenceContainer.h \</span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="plaintext"> computePijComponent.h multipleStochasticProcess.h gammaDistribution.h \</span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="plaintext"> generalGammaDistribution.h likelihoodComputation.h suffStatComponent.h \</span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="plaintext"> likelihoodComputationGL.h computeUpAlg.h</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="plaintext">likelihoodComputationGL.o likelihoodComputationGL.debug.o: likelihoodComputationGL.cpp \</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="plaintext"> likelihoodComputationGL.h definitions.h computePijComponent.h tree.h \</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h computeUpAlg.h \</span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="plaintext"> likelihoodComputation.h</span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="plaintext">threeStateModel.o threeStateModel.debug.o: threeStateModel.cpp threeStateModel.h definitions.h \</span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="plaintext"> replacementModel.h fromQtoPt.h errorMsg.h matrixUtils.h logFile.h \</span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="plaintext"> someUtil.h alphabet.h</span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="plaintext">threeStateAlphabet.o threeStateAlphabet.debug.o: threeStateAlphabet.cpp threeStateAlphabet.h \</span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="plaintext"> alphabet.h errorMsg.h</span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="plaintext">oneTwoMoreModel.o oneTwoMoreModel.debug.o: oneTwoMoreModel.cpp oneTwoMoreModel.h definitions.h \</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="plaintext"> replacementModel.h fromQtoPt.h errorMsg.h matrixUtils.h logFile.h \</span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="plaintext"> someUtil.h alphabet.h</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="plaintext">betaDistributionFixedCategories.o betaDistributionFixedCategories.debug.o: betaDistributionFixedCategories.cpp \</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="plaintext"> betaDistributionFixedCategories.h definitions.h betaDistribution.h \</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="plaintext"> distribution.h errorMsg.h gammaUtilities.h numRec.h \</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="plaintext"> uniformDistribution.h logFile.h</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="plaintext">betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.debug.o: \</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="plaintext"> betaDistributionFixedCategoriesWithOmegaUniform.cpp \</span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="plaintext"> betaDistributionFixedCategoriesWithOmegaUniform.h definitions.h \</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="plaintext"> betaDistributionFixedCategories.h betaDistribution.h distribution.h \</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="plaintext"> errorMsg.h uniformDistribution.h gammaUtilities.h numRec.h logFile.h \</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="plaintext"> matrixUtils.h</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="plaintext">bblEM2codon.o bblEM2codon.debug.o: bblEM2codon.cpp bblEM2codon.h definitions.h tree.h \</span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="plaintext"> replacementModel.h distribution.h sequenceContainer.h sequence.h \</span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="plaintext"> alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="plaintext"> countTableComponent.h computePijComponent.h multipleStochasticProcess.h \</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h suffStatComponent.h \</span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="plaintext"> likelihoodComputation.h unObservableData.h likelihoodComputation2Codon.h \</span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="plaintext"> fromCountTableComponentToDistance2Codon.h computeUpAlg.h \</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="plaintext"> computeDownAlg.h computeCounts.h treeIt.h</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="plaintext">bestAlphaAndK.o bestAlphaAndK.debug.o: bestAlphaAndK.cpp bestAlphaAndK.h definitions.h tree.h \</span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h likelihoodComputation.h \</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="plaintext"> computePijComponent.h stochasticProcess.h pijAccelerator.h \</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h likelihoodComputation2Codon.h \</span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="plaintext"> wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h bblEM2codon.h \</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext"> countTableComponent.h computeUpAlg.h numRec.h uniformDistribution.h \</span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="plaintext"> betaOmegaDistribution.h betaDistribution.h codonUtils.h nucleotide.h \</span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="plaintext"> amino.h fastaFormat.h clustalFormat.h recognizeFormat.h \</span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="plaintext"> evaluateCharacterFreq.h</span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="plaintext">fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.debug.o: \</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext"> fromCountTableComponentToDistance2Codon.cpp \</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="plaintext"> fromCountTableComponentToDistance2Codon.h definitions.h \</span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="plaintext"> countTableComponent.h stochasticProcess.h pijAccelerator.h \</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="plaintext"> replacementModel.h distribution.h likeDist2Codon.h distanceMethod.h \</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="plaintext"> sequence.h errorMsg.h alphabet.h mulAlphabet.h someUtil.h logFile.h \</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="plaintext"> wYangModel.h fromQtoPt.h codon.h geneticCodeHolder.h likeDist.h \</span>
</pre>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="plaintext"> jcDistance.h unObservableData.h tree.h readTree.h sequenceContainer.h \</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="plaintext"> gainLossAlphabet.h computePijComponent.h multipleStochasticProcess.h \</span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h</span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="plaintext">gtrModel.o gtrModel.debug.o: gtrModel.cpp gtrModel.h replacementModel.h definitions.h \</span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="plaintext"> fromQtoPt.h readDatMatrix.h datMatrixHolder.h errorMsg.h matrixUtils.h \</span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="plaintext"> logFile.h</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="plaintext">bestGtrModelParams.o bestGtrModelParams.debug.o: bestGtrModelParams.cpp bestGtrModelParams.h \</span>
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="plaintext"> definitions.h likelihoodComputation.h computePijComponent.h tree.h \</span>
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="plaintext"> replacementModel.h distribution.h multipleStochasticProcess.h \</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="plaintext"> gammaDistribution.h generalGammaDistribution.h sequenceContainer.h \</span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="plaintext"> sequence.h alphabet.h mulAlphabet.h someUtil.h gainLossAlphabet.h \</span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext"> suffStatComponent.h unObservableData.h gtrModel.h fromQtoPt.h bblEM.h \</span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="plaintext"> countTableComponent.h bblEMProportionalEB.h bblLSProportionalEB.h \</span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="plaintext"> numRec.h uniformDistribution.h bestAlpha.h</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="plaintext">simulateRateShiftJumps.o simulateRateShiftJumps.debug.o: simulateRateShiftJumps.cpp \</span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="plaintext"> simulateRateShiftJumps.h simulateJumpsAbstract.h definitions.h tree.h \</span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="plaintext"> readTree.h errorMsg.h logFile.h stochasticProcess.h pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="plaintext"> replacementModel.h distribution.h alphabet.h mulAlphabet.h someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="plaintext"> talRandom.h replacementModelSSRV.h fromQtoPt.h \</span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="plaintext"> generalGammaDistribution.h</span>
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="plaintext">integerAlphabet.o integerAlphabet.debug.o: integerAlphabet.cpp integerAlphabet.h alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="plaintext"> errorMsg.h logFile.h someUtil.h definitions.h</span></pre>
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<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#678cc88c16875a978296761818f173170fc6e7e2"><strong>libs/phylogeny/someUtil.cpp</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// $Id: someUtil.cpp 1<span class="idiff left right">1906 2013-12-26 10:12:24Z itayma</span>y $</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// $Id: someUtil.cpp 1<span class="idiff left right">5479 2016-10-10 16:25:21Z elilev</span>y $</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "someUtil.h"</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "errorMsg.h"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -226,13 +226,17 @@ bool isCharInString(const string& stringToCheck, const char charToCheck) {</td>
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226
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="nf" style="color: #900; font-weight: 600;">double2string</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lenght</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">round</span><span class="p">){</span></span>
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227
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// first getting the integer part:</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Itay: fixing bug regarding negative floats </span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x_abs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">theIntegerPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">x_abs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">theRemainingPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fabs</span><span class="p">(</span><span class="n" style="color: #333;">x_abs</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">theIntegerPart</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">integerRepresentingTheRemainingPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">theRemainingPart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mf" style="color: #099;">10.0</span><span class="p">,</span><span class="n" style="color: #333;">lenght</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp"> <span class="n" style="color: #333;">integerRepresentingTheRemainingPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">theRemainingPart</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mf" style="color: #099;">10.0</span><span class="p">,</span><span class="n" style="color: #333;">lenght</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">integerRepresentingTheRemainingPart</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mf" style="color: #099;">10.0</span><span class="p">,</span><span class="n" style="color: #333;">lenght</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="n" style="color: #333;">integerRepresentingTheRemainingPart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">theIntegerPart</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">part1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">int2string</span><span class="p">(</span><span class="n" style="color: #333;">theIntegerPart</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">part2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">int2string</span><span class="p">(</span><span class="n" style="color: #333;">integerRepresentingTheRemainingPart</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -353,7 +357,7 @@ MDOUBLE string2double(const string& inString) {</td>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">checkThatFileExist</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fileName</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">file1</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">file1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">file1</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">good</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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357
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">file1</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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358
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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359
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -401,7 +405,7 @@ string* searchStringInFile(const string& string2find,</td>
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401
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">inFileName</span><span class="p">)</span> <span class="p">{</span></span>
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402
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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403
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">inFileName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span> <span class="p">{</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">good</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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405
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Unable to open file name: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">inFileName</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" in function searchStringInFile"</span><span class="p">;</span> </span>
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406
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">errorMsg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reportError</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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407
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -428,7 +432,7 @@ string* searchStringInFile(const string& string2find,</td>
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428
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">inFileName</span><span class="p">)</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">// return the string that is AFTER the string to search.</span></span>
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429
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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430
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">inFileName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span> <span class="p">{</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">good</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
432
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Unable to open file name: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">inFileName</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" in function searchStringInFile"</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">errorMsg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reportError</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -452,7 +456,7 @@ string* searchStringInFile(const string& string2find,</td>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">doesWordExistInFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">string2find</span><span class="p">,</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">inFileName</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="n" style="color: #333;">ifstream</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">inFileName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">f</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span> <span class="p">{</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">good</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Unable to open file name: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">inFileName</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">" in function searchStringInFile"</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">errorMsg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reportError</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#0007d31d42c492deef7cdbecee9f101624baedb5"><strong>programs/Makefile.generic</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,8 +53,8 @@ GENGETOPT = gengetopt</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="make"><span class="nl">.SECONDARY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(addsuffix _cmdline.c</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">$(EXEC)) $(addsuffix _cmdline.h</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">$(EXEC)) $(addsuffix .ggo</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">$(EXEC))</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(libDir)</span> <span class="nt" style="color: #000080;">-DLOG</span> <span class="nt" style="color: #000080;"><span class="idiff left right">-ftemplate-depth-32</span></span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGSDEBUG</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(libDir)</span> <span class="nt" style="color: #000080;">-DLOG</span> <span class="nt" style="color: #000080;"><span class="idiff left right">-ftemplate-depth-32</span></span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(libDir)</span> <span class="nt" style="color: #000080;">-DLOG</span> </span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="make"><span class="nv" style="color: #008080;">CPPFLAGSDEBUG</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wno-sign-compare</span> <span class="nt" style="color: #000080;">-I</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-I</span><span class="nv" style="color: #008080;">$(libDir)</span> <span class="nt" style="color: #000080;">-DLOG</span> </span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="make"></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGSDEBUG</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nt" style="color: #000080;">-g</span> </span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># sources</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -196,7 +196,7 @@ pl:</td>
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196
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$(LIB)</span></span>
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197
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="make"></span>
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198
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="make"></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="make"><span class="nl">%.debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG <span class="idiff left right">-ftemplate-depth-25</span></span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="make"><span class="nl">%.debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">CPPFLAGS = -g -Wall -Wno-sign-compare -I. -I../.. -DLOG </span></span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="make"></span>
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201
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="make"><span class="nl">%.debug</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.o </span></span>
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202
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#179fb1eeb60770928e6ec5fcc14eca2655108e6d"><strong>programs/fastml/bbReport.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,7 +47,7 @@ void BandBReport::makeReport() const {</td>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;"><<</span><span class="s" style="color: #d14;">" position is: "</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">_position</span><span class="o" style="font-weight: 600;"><<</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cerr<<"reportFileIs: "<<_reportFileName<<endl;</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">out</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span> <span class="p">{</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">out</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">good</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">errorMsg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reportError</span><span class="p">(</span><span class="s" style="color: #d14;">"unable to open output file for reporting"</span><span class="p">);</span></span>
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="p">}</span></span>
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// exit(555);</span></span>
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<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#239a1f618d88854b9554db94a08a5737bdc9bc85"><strong>programs/fastml/make.dep</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fastml.o fastml.debug.o: fastml.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h bb_options_list.h \</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> ../../libs/phylogeny/geneticCodeHolder.h \</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> sequenceDataDiff.h ../../libs/phylogeny/amino.h \</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ../../libs/phylogeny/codon.h ../../libs/phylogeny/recognizeFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h bbAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h bbNodeOrderAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> bbfindBestAVDynProg.h bbReport.h ../../libs/phylogeny/distribution.h</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">bbAlg.o bbAlg.debug.o: bbAlg.cpp bbAlg.h ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h bb_options.h \</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> ../../libs/phylogeny/getopt.h bb_options_list.h \</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h bbEvaluateSpecificAV.h \</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> bbReport.h ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> ../../libs/phylogeny/maseFormat.h</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">bbComputeDownAlg.o bbComputeDownAlg.debug.o: bbComputeDownAlg.cpp bbComputeDownAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h ../../libs/phylogeny/alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">bbComputeUpAlg.o bbComputeUpAlg.debug.o: bbComputeUpAlg.cpp bbComputeUpAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">bbEvaluateSpecificAV.o bbEvaluateSpecificAV.debug.o: bbEvaluateSpecificAV.cpp bbEvaluateSpecificAV.h \</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> bb_options.h ../../libs/phylogeny/getopt.h \</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h bb_options_list.h \</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/sequenceContainer.h \</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">bbfindBestAVDynProg.o bbfindBestAVDynProg.debug.o: bbfindBestAVDynProg.cpp bbfindBestAVDynProg.h \</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> bb_options.h ../../libs/phylogeny/getopt.h \</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h bb_options_list.h \</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">bbNodeOrderAlg.o bbNodeOrderAlg.debug.o: bbNodeOrderAlg.cpp bbNodeOrderAlg.h \</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h bb_options.h \</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> ../../libs/phylogeny/getopt.h bb_options_list.h \</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/sequence.h \</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h bbComputeUpAlg.h \</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> bbComputeDownAlg.h ../../libs/phylogeny/computeMarginalAlg.h \</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">bb_options.o bb_options.debug.o: bb_options.cpp bb_options.h ../../libs/phylogeny/getopt.h \</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h bb_options_list.h \</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">bbReport.o bbReport.debug.o: bbReport.cpp bbReport.h ../../libs/phylogeny/definitions.h \</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> ../../libs/phylogeny/amino.h ../../libs/phylogeny/definitions.h \</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> ../../libs/phylogeny/geneticCodeHolder.h ../../libs/phylogeny/codon.h \</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> ../../libs/phylogeny/nucleotide.h ../../libs/phylogeny/codon.h</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">computeMarginalReconstruction.o computeMarginalReconstruction.debug.o: computeMarginalReconstruction.cpp \</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> computeMarginalReconstruction.h ../../libs/phylogeny/definitions.h \</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/tree.h \</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> ../../libs/phylogeny/computeMarginalAlg.h ../../libs/phylogeny/treeIt.h</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">jointNoGamma.o jointNoGamma.debug.o: jointNoGamma.cpp jointNoGamma.h \</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/readTree.h \</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h suffStatComponentJointNoGamma.h \</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/seqContainerTreeMap.h \</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/sequenceContainer.h</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">mainbb.o mainbb.debug.o: mainbb.cpp mainbb.h bb_options.h ../../libs/phylogeny/getopt.h \</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h bb_options_list.h \</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/codon.h \</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> ../../libs/phylogeny/geneticCodeHolder.h \</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h ../../libs/phylogeny/aaJC.h \</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> ../../libs/phylogeny/amino.h ../../libs/phylogeny/codon.h bbAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h bbNodeOrderAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h bbEvaluateSpecificAV.h \</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h bbfindBestAVDynProg.h \</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> bbReport.h ../../libs/phylogeny/distribution.h \</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> ../../libs/phylogeny/bestAlpha.h \</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bblEM.h \</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> ../../libs/phylogeny/clustalFormat.h computeMarginalReconstruction.h \</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h ../../libs/phylogeny/fastaFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h jointNoGamma.h \</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> suffStatComponentJointNoGamma.h ../../libs/phylogeny/likeDist.h \</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> ../../libs/phylogeny/maseFormat.h ../../libs/phylogeny/molphyFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> ../../libs/phylogeny/nexusFormat.h ../../libs/phylogeny/nucleotide.h \</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/nj.h \</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/gtrModel.h \</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/hky.h \</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> ../../libs/phylogeny/phylipFormat.h ../../libs/phylogeny/readDatMatrix.h \</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h \</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h \</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> ../../libs/phylogeny/bestGtrModelParams.h \</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> ../../libs/phylogeny/gtrModel.h ../../libs/phylogeny/bestTamura92param.h \</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> ../../libs/phylogeny/tamura92.h ../../libs/phylogeny/bestHKYparam.h \</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> ../../libs/phylogeny/hky.h ../../libs/phylogeny/bestAlphaAndK.h \</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation2Codon.h \</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> ../../libs/phylogeny/wYangModel.h ../../libs/phylogeny/bblEM2codon.h \</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> ../../libs/phylogeny/codonUtils.h ../../libs/phylogeny/nucleotide.h \</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> ../../libs/phylogeny/amino.h ../../libs/phylogeny/fastaFormat.h \</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> ../../libs/phylogeny/clustalFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">sequenceDataDiff.o sequenceDataDiff.debug.o: sequenceDataDiff.cpp sequenceDataDiff.h \</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/gainLossAlphabet.h</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.debug.o: suffStatComponentJointNoGamma.cpp \</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> suffStatComponentJointNoGamma.h ../../libs/phylogeny/definitions.h</span></pre>
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<li id="e3ae4d8826cc1b107e6e2dafc15891afd34309fc">
<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#e3ae4d8826cc1b107e6e2dafc15891afd34309fc"><strong>programs/gainLoss/make.dep</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gainLossOptions.o gainLossOptions.debug.o: gainLossOptions.cpp gainLossOptions.h \</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/errorMsg.h \</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> ../../libs/phylogeny/Parameters.h</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">gainLoss.o gainLoss.debug.o: gainLoss.cpp computePosteriorExpectationOfChange.h \</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/simulateJumps.h \</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> ../../libs/phylogeny/simulateJumpsAbstract.h \</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> ../../libs/phylogeny/computeJumps.h ../../libs/phylogeny/someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h gainLoss.h \</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computeUpAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h gainLossOptimizer.h \</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> ../../libs/phylogeny/simulateTree.h ../../libs/phylogeny/phylipFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> ../../libs/phylogeny/maseFormat.h ../../libs/phylogeny/fastaFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> ../../libs/phylogeny/clustalFormat.h rate4siteGL.h gainLoss4site.h \</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> siteSpecificGL.h computeCountsGL.h computeCorrelations.h \</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> ../../libs/phylogeny/Parameters.h \</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> ../../libs/phylogeny/extremeValDistribution.h simulateOnePos.h \</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/threeStateModel.h \</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> ../../libs/phylogeny/oneTwoMoreModel.h sankoffReconstructGL.h bblLS.h \</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> ../../libs/phylogeny/bblEMfixRoot.h</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">gainLossUtils.o gainLossUtils.debug.o: gainLossUtils.cpp gainLossUtils.h \</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h \</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/matrixUtils.h \</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> gainLossModel.h ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h \</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> ../../libs/phylogeny/Parameters.h</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">optimizeGainLossModel.o optimizeGainLossModel.debug.o: optimizeGainLossModel.cpp \</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/bblEM.h \</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/definitions.h \</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"> gainLossModel.h ../../libs/phylogeny/replacementModel.h \</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h \</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/Parameters.h</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">optimizeGainLossModelVV.o optimizeGainLossModelVV.debug.o: optimizeGainLossModelVV.cpp \</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> optimizeGainLossModelVV.h ../../libs/phylogeny/bblEM.h \</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/definitions.h \</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> gainLossModel.h ../../libs/phylogeny/replacementModel.h \</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> ../../libs/phylogeny/Parameters.h</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">likelihoodComputationGL.o likelihoodComputationGL.debug.o: \</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.cpp \</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">gainLossModel.o gainLossModel.debug.o: gainLossModel.cpp gainLossModel.h \</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/fromQtoPt.h \</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h gainLossUtils.h gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">siteSpecificGL.o siteSpecificGL.debug.o: siteSpecificGL.cpp siteSpecificGL.h \</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> ../../libs/phylogeny/numRec.h ../../libs/phylogeny/uniformDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h gainLossUtils.h gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h \</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h gainLossModel.h \</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h gainLossOptions.h</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.debug.o: \</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"> computePosteriorExpectationOfChange.cpp \</span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"> computePosteriorExpectationOfChange.h ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext"> ../../libs/phylogeny/simulateJumps.h \</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"> ../../libs/phylogeny/simulateJumpsAbstract.h \</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> ../../libs/phylogeny/computeJumps.h ../../libs/phylogeny/someUtil.h \</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/matrixUtils.h \</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h \</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h gainLossOptions.h \</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"> gainLossModel.h ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> gainLossUtils.h gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h \</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">gainLossProject.o gainLossProject.debug.o: gainLossProject.cpp gainLoss.h \</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext"> ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/bblEM.h \</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/distanceTable.h \</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \</span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext"> gainLossOptions.h ancestralReconstructStates.h \</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext"> computePosteriorExpectationOfChange.h \</span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext"> ../../libs/phylogeny/simulateJumps.h \</span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext"> ../../libs/phylogeny/simulateJumpsAbstract.h \</span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"> ../../libs/phylogeny/computeJumps.h \</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext"> ../../libs/phylogeny/Parameters.h</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext">gainLossOptimizer.o gainLossOptimizer.debug.o: gainLossOptimizer.cpp gainLossOptimizer.h \</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h gainLoss.h \</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext"> ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext"> ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \</span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \</span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext"> gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext"> gainLossOptions.h ancestralReconstructStates.h \</span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h \</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext"> ../../libs/phylogeny/bblEMfixRoot.h bblLS.h</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">ancestralReconstructStates.o ancestralReconstructStates.debug.o: ancestralReconstructStates.cpp \</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext"> ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/suffStatComponent.h \</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h gainLossAlphabet.h \</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h \</span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h ../../libs/phylogeny/someUtil.h \</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext">rate4siteGL.o rate4siteGL.debug.o: rate4siteGL.cpp rate4siteGL.h \</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h gainLoss.h \</span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext"> ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"> ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \</span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext"> gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext"> gainLossOptions.h ancestralReconstructStates.h \</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext">computeCountsGL.o computeCountsGL.debug.o: computeCountsGL.cpp computeCountsGL.h \</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h gainLoss.h \</span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="plaintext"> ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext"> ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \</span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext"> gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext"> gainLossOptions.h ancestralReconstructStates.h \</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="plaintext"> computePosteriorExpectationOfChange.h \</span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="plaintext"> ../../libs/phylogeny/simulateJumps.h \</span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="plaintext"> ../../libs/phylogeny/simulateJumpsAbstract.h \</span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="plaintext"> ../../libs/phylogeny/computeJumps.h \</span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h</span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext">computeCorrelations.o computeCorrelations.debug.o: computeCorrelations.cpp computeCorrelations.h \</span>
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<pre style="margin: 0;">+<span id="LC661" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/Parameters.h \</span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="plaintext"> gainLoss.h ../../libs/phylogeny/aaJC.h \</span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/bblEM.h \</span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/readTree.h \</span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \</span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="plaintext"> gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \</span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \</span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="plaintext"> gainLossOptions.h ancestralReconstructStates.h \</span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h \</span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="plaintext"> ../../libs/phylogeny/extremeValDistribution.h</span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="plaintext">gainLoss4site.o gainLoss4site.debug.o: gainLoss4site.cpp gainLoss4site.h \</span>
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731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h gainLoss.h \</span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="plaintext"> ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/replacementModel.h \</span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="plaintext"> ../../libs/phylogeny/bblEM.h ../../libs/phylogeny/tree.h \</span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \</span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="plaintext"> gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \</span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/tree.h \</span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="plaintext"> ../../libs/phylogeny/treeIt.h ../../libs/phylogeny/trivialAccelerator.h \</span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="plaintext"> gainLossOptions.h ancestralReconstructStates.h \</span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="plaintext"> ../../libs/phylogeny/computeDownAlg.h \</span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/unObservableData.h \</span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h siteSpecificGL.h</span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="plaintext">simulateChangesAlongTree.o simulateChangesAlongTree.debug.o: simulateChangesAlongTree.cpp \</span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="plaintext"> simulateChangesAlongTree.h ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \</span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/stochasticProcess.h \</span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h ../../libs/phylogeny/alphabet.h \</span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h ../../libs/phylogeny/matrixUtils.h \</span>
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810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext"> gainLoss.h ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \</span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/stochasticProcess.h \</span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h \</span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="plaintext"> ../../libs/phylogeny/fastStartTree.h gainLossAlphabet.h gainLossModel.h \</span>
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831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \</span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="plaintext"> gainLossUtils.h ../../libs/phylogeny/gammaDistribution.h \</span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \</span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h gainLossOptions.h \</span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="plaintext"> ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \</span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h \</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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849
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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850
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<pre style="margin: 0;">+<span id="LC850" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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<pre style="margin: 0;">+<span id="LC851" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h \</span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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862
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<pre style="margin: 0;">+<span id="LC862" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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863
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h \</span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h</span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="plaintext">simulateOnePos.o simulateOnePos.debug.o: simulateOnePos.cpp ../../libs/phylogeny/definitions.h \</span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="plaintext"> simulateOnePos.h ../../libs/phylogeny/tree.h \</span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/readTree.h \</span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/logFile.h \</span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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873
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<pre style="margin: 0;">+<span id="LC873" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/mulAlphabet.h \</span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/threeStateModel.h \</span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="plaintext"> ../../libs/phylogeny/fromQtoPt.h ../../libs/phylogeny/matrixUtils.h \</span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="plaintext"> ../../libs/phylogeny/oneTwoMoreModel.h \</span>
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="plaintext"> ../../libs/phylogeny/simulateTree.h ../../libs/phylogeny/tree.h \</span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="plaintext"> ../../libs/phylogeny/threeStateAlphabet.h \</span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h \</span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="plaintext"> ../../libs/phylogeny/uniDistribution.h ../../libs/phylogeny/sequence.h \</span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="plaintext"> simulateChangesAlongTree.h ../../libs/phylogeny/treeIt.h \</span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="plaintext"> ../../libs/phylogeny/fastaFormat.h gainLoss.h \</span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="plaintext"> ../../libs/phylogeny/aaJC.h ../../libs/phylogeny/bblEM.h \</span>
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890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="plaintext"> ../../libs/phylogeny/countTableComponent.h \</span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/bestAlpha.h \</span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="plaintext"> ../../libs/phylogeny/chebyshevAccelerator.h \</span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctors.h \</span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="plaintext"> ../../libs/phylogeny/checkcovFanctorsWithFactors.h \</span>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationFactors.h \</span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="plaintext"> ../../libs/phylogeny/distanceTable.h \</span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="plaintext"> ../../libs/phylogeny/distanceMethod.h \</span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h ../../libs/phylogeny/fastStartTree.h \</span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="plaintext"> gainLossAlphabet.h gainLossModel.h \</span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h ../../libs/phylogeny/fromQtoPt.h \</span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h gainLossUtils.h \</span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h \</span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h gainLossOptions.h \</span>
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921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="plaintext"> ancestralReconstructStates.h ../../libs/phylogeny/computeDownAlg.h \</span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h ../../libs/phylogeny/likeDist.h \</span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="plaintext"> ../../libs/phylogeny/jcDistance.h \</span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/nj.h \</span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="plaintext"> ../../libs/phylogeny/njConstrain.h ../../libs/phylogeny/distances2Tree.h \</span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="plaintext"> ../../libs/phylogeny/nucJC.h ../../libs/phylogeny/numRec.h \</span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="plaintext"> optimizeGainLossModel.h ../../libs/phylogeny/computePijComponent.h \</span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h ../../libs/phylogeny/talRandom.h \</span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h optimizeGainLossModelVV.h \</span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="plaintext"> ../../libs/phylogeny/readDatMatrix.h \</span>
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936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="plaintext"> ../../libs/phylogeny/datMatrixHolder.h \</span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="plaintext"> ../../libs/phylogeny/siteSpecificRate.h</span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="plaintext">bblLS.o bblLS.debug.o: bblLS.cpp bblLS.h ../../libs/phylogeny/definitions.h \</span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \</span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/sequenceContainer.h \</span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h ../../libs/phylogeny/alphabet.h \</span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \</span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h ../../libs/phylogeny/tree.h \</span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h gainLossUtils.h \</span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="plaintext"> gainLossAlphabet.h ../../libs/phylogeny/gammaDistribution.h \</span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/matrixUtils.h \</span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/treeIt.h \</span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h ../../libs/phylogeny/numRec.h \</span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputation.h \</span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="plaintext"> ../../libs/phylogeny/suffStatComponent.h \</span>
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973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="plaintext"> ../../libs/phylogeny/likelihoodComputationGL.h \</span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="plaintext"> ../../libs/phylogeny/computeUpAlg.h gainLossOptions.h</span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="plaintext">sankoffReconstructGL.o sankoffReconstructGL.debug.o: sankoffReconstructGL.cpp sankoffReconstructGL.h \</span>
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="plaintext"> ../../libs/phylogeny/tree.h ../../libs/phylogeny/definitions.h \</span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="plaintext"> ../../libs/phylogeny/readTree.h ../../libs/phylogeny/errorMsg.h \</span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/logFile.h \</span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/alphabet.h \</span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h \</span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="plaintext"> ../../libs/phylogeny/pijAccelerator.h \</span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="plaintext"> ../../libs/phylogeny/replacementModel.h \</span>
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984
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<pre style="margin: 0;">+<span id="LC984" class="line" lang="plaintext"> ../../libs/phylogeny/distribution.h \</span>
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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h ../../libs/phylogeny/someUtil.h \</span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h gainLossUtils.h \</span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="plaintext"> gainLossAlphabet.h ../../libs/phylogeny/gammaDistribution.h \</span>
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989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistribution.h \</span>
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990
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<pre style="margin: 0;">+<span id="LC990" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistributionFixedCategories.h \</span>
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991
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<pre style="margin: 0;">+<span id="LC991" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionFixedCategories.h \</span>
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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="plaintext"> ../../libs/phylogeny/GamMixtureOptimizer.h \</span>
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993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="plaintext"> ../../libs/phylogeny/stochasticProcess.h \</span>
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994
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<pre style="margin: 0;">+<span id="LC994" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/tree.h \</span>
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995
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<pre style="margin: 0;">+<span id="LC995" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h \</span>
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996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="plaintext"> ../../libs/phylogeny/unObservableData.h \</span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="plaintext"> ../../libs/phylogeny/computePijComponent.h \</span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="plaintext"> ../../libs/phylogeny/multipleStochasticProcess.h \</span>
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="plaintext"> ../../libs/phylogeny/gammaDistribution.h \</span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="plaintext"> ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h \</span>
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1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="plaintext"> ../../libs/phylogeny/distributionPlusInvariant.h \</span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="plaintext"> ../../libs/phylogeny/gammaUtilities.h ../../libs/phylogeny/numRec.h \</span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="plaintext"> ../../libs/phylogeny/uniformDistribution.h \</span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h \</span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="plaintext"> ../../libs/phylogeny/mixtureDistribution.h ../../libs/phylogeny/treeIt.h \</span>
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1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="plaintext"> ../../libs/phylogeny/evaluateCharacterFreq.h \</span>
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1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="plaintext"> ../../libs/phylogeny/trivialAccelerator.h \</span>
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1008
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<pre style="margin: 0;">+<span id="LC1008" class="line" lang="plaintext"> ../../libs/phylogeny/threeStateAlphabet.h \</span>
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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="plaintext"> ../../libs/phylogeny/sequence.h ../../libs/phylogeny/recognizeFormat.h \</span>
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1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="plaintext"> ../../libs/phylogeny/seqContainerTreeMap.h ../../libs/phylogeny/treeIt.h \</span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="plaintext"> ../../libs/phylogeny/treeUtil.h ../../libs/phylogeny/amino.h \</span>
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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="plaintext"> ../../libs/phylogeny/geneticCodeHolder.h ../../libs/phylogeny/codon.h \</span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="plaintext"> ../../libs/phylogeny/nucleotide.h ../../libs/phylogeny/integerAlphabet.h \</span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="plaintext"> gainLossOptions.h</span></pre>
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<a href="https://salsa.debian.org/med-team/fastml/commit/05b005104a551602c63d3605b9a873cf9f9802ad#8666366720e38d2d816682f2ebaca796912d92dc"><strong>programs/indelCoder/make.dep</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">indelCoder.o indelCoder.debug.o: indelCoder.cpp indelCoder.h gaps.h \</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h character.h \</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> indelCoderOptions.h ../../libs/phylogeny/amino.h \</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h \</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h indelCoderUtils.h</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">indelCoderOptions.o indelCoderOptions.debug.o: indelCoderOptions.cpp indelCoderOptions.h \</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/errorMsg.h \</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ../../libs/phylogeny/someUtil.h ../../libs/phylogeny/logFile.h \</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/alphabet.h \</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ../../libs/phylogeny/Parameters.h</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">indelCoderProject.o indelCoderProject.debug.o: indelCoderProject.cpp indelCoder.h gaps.h \</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h character.h \</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> indelCoderOptions.h ../../libs/phylogeny/amino.h \</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h \</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/logFile.h \</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h indelCoderUtils.h \</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> ../../libs/phylogeny/Parameters.h</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">indelCoderUtils.o indelCoderUtils.debug.o: indelCoderUtils.cpp indelCoderUtils.h \</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h indelCoder.h gaps.h \</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h character.h \</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> ../../libs/phylogeny/matrixUtils.h ../../libs/phylogeny/definitions.h \</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> ../../libs/phylogeny/logFile.h ../../libs/phylogeny/errorMsg.h \</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> indelCoderOptions.h ../../libs/phylogeny/amino.h \</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> ../../libs/phylogeny/alphabet.h ../../libs/phylogeny/geneticCodeHolder.h \</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> ../../libs/phylogeny/codon.h ../../libs/phylogeny/someUtil.h \</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h ../../libs/phylogeny/sequence.h \</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> ../../libs/phylogeny/mulAlphabet.h \</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> ../../libs/phylogeny/gainLossAlphabet.h \</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> ../../libs/phylogeny/recognizeFormat.h \</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> ../../libs/phylogeny/sequenceContainer.h \</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> ../../libs/phylogeny/talRandom.h</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">character.o character.debug.o: character.cpp character.h ../../libs/phylogeny/definitions.h \</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> gaps.h ../../libs/phylogeny/matrixUtils.h \</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> ../../libs/phylogeny/definitions.h ../../libs/phylogeny/logFile.h \</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> ../../libs/phylogeny/errorMsg.h indelCoderOptions.h</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">gaps.o gaps.debug.o: gaps.cpp gaps.h ../../libs/phylogeny/definitions.h</span></pre>
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