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data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:154: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:154: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:158: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:202: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:232: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:241: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:250: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:275: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/DivergenceDating/DivergenceDatingTutorial.tex:315: BEAUti ==> beauty 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data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:51: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:52: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:64: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:66: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:70: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:70: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:70: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:78: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:146: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:146: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:152: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:267: paremeters ==> parameters data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:415: overlayed ==> overlaid data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STACEY/STACEY_tutorial.tex:533: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:45: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:57: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:59: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:61: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:63: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:65: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:65: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:71: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:139: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:139: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:145: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:260: paremeters ==> parameters data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:408: overlayed ==> overlaid data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:526: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:535: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:539: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/doc/tutorials/STARBEAST/StarBEAST_tutorial.tex:541: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/testYuleCalibrated.xml:145: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/examples/testYuleUncalibrated.xml:144: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testBSPNoClock.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testBirthDeathModel_10taxa.xml:20: intialize ==> initialize data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testCalibration.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testCoalescent.xml:32: intialize ==> initialize data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testCoalescentNoClock.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testCoalescentNoClock1.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testEBSP.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testExponentialGrowth.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testMultiSubstModel.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testRandomLocalClock.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testSRD06CP12_3.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testStarBEASTConstant.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testStarBEASTLinear.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testStarBEASTLinearConstRoot.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testStrictClockNoDate.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testStrictClockNoDate2.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testStrictClockTipDatesSampling.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testStrictClockTipTime.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testUCRelaxedClockLogNormal.xml:3: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testYule.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/beast2vs1/beast1/testYuleModel_10taxa.xml:20: intialize ==> initialize data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY1044.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY1366.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY1510.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY1748.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY1749.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY1809.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY336.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY3475.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY501.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY520.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY755.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/benchmark/1/testHKY767.xml:2: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/examples/nexus/angiosperms.nex:6: OTU ==> OUT data/beast2-mcmc-2.6.3+dfsg/examples/nexus/seaview.nxs:550: OT ==> TO, OF, OR data/beast2-mcmc-2.6.3+dfsg/examples/parameterised/RSV2.json:3: singe ==> single data/beast2-mcmc-2.6.3+dfsg/release/Linux/bin/beauti:32: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Linux/jrebin/beauti:33: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Mac/launch.c:7: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Mac/launch.c:56: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Mac/launch.c:57: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Mac/launch.c:61: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Windows/BEAUti_launch4j.xml:3: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Windows/BEAUti_launch4j.xml:5: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Windows/BEAUti_launch4j_jre.xml:3: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Windows/BEAUti_launch4j_jre.xml:5: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Windows/bat/beauti.bat:5: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/Windows/bat/beauti.bat:9: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:33: behavour ==> behaviour data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:62: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:67: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:71: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:71: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:75: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:89: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:133: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:134: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/README.txt:176: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:19: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:26: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:37: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:84: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:85: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:94: preven ==> prevent data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:104: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:139: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:156: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:181: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:189: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:213: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:224: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:247: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:263: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:283: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:304: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:328: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:331: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:346: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:365: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:365: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:371: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:381: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:400: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:413: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/release/common/VERSION HISTORY.txt:431: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/BeastMCMC.java:31: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/BeastMCMC.java:31: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/BeastMCMC.java:32: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/BeastMCMC.java:498: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/BeastMCMC.java:508: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beastapp/BeastDialog.java:243: alway ==> always data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beastapp/BeastMain.java:132: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beastapp/BeastMain.java:135: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beastapp/BeastMain.java:137: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/AlignmentImporter.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/AlignmentListInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/AlignmentViewer.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java:107: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java:109: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java:264: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiAlignmentProvider.java:645: implicitely ==> implicitly data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:23: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:23: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:24: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:35: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:37: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:41: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:47: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:127: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:129: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:137: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:139: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:141: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:142: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConfig.java:144: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConnector.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConnector.java:21: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConnector.java:31: suplied ==> supplied data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiConnector.java:32: suplied ==> supplied data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:86: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:131: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:131: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:210: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:210: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:597: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:762: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:772: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:798: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:817: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:819: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:821: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:935: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:1015: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:2345: deLink ==> unlink data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:2413: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:2413: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:2414: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:2414: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:2418: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDoc.java:2421: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiDocListener.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiHelpAction.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiHelpAction.java:8: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiLauncher.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiLauncher.java:11: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiLauncher.java:11: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiLauncher.java:20: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiLauncher.java:24: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiLauncher.java:24: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanel.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanel.java:25: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanel.java:41: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanel.java:46: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanel.java:424: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanelConfig.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanelConfig.java:21: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanelConfig.java:36: deafult ==> default data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanelConfig.java:42: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiPanelConfig.java:232: mathing ==> matching data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:43: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:86: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:157: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:158: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:220: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:222: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:252: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/BeautiSubTemplate.java:358: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/ClockModelListInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/ClonePartitionPanel.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/ClonePartitionPanel.java:14: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/ConstantPopulationInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Fragment.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Fragment.java:13: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/FrequenciesInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/GeneTreeForSpeciesTreeDistributionInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/GuessPatternDialog.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/GuessPatternDialog.java:212: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:36: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:286: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:314: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:316: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:367: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:375: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageDialog.java:377: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/JPackageRepositoryDialog.java:19: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/LoggerListInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/MRCAPriorInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/MRCAPriorInputEditor.java:77: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/OperatorListInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/ParametricDistributionInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/PartitionContext.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/PriorInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/PriorListInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/PriorListInputEditor.java:317: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/PriorProvider.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/SiteModelInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/SiteModelInputEditor.java:163: accross ==> across data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/SiteModelInputEditor.java:167: accross ==> across data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/SpeciesTreePriorInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/StateNodeInitialiserListInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/StateNodeListInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/TaxonSetDialog.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/TaxonSetInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/TipDatesInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/TipDatesInputEditor.java:363: selectin ==> selection, selecting data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/TreeDistributionInputEditor.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/WrappedOptionPane.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:7: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:51: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:53: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:107: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:112: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:123: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:429: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:436: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:438: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:462: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:613: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:649: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:805: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1183: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1184: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1197: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1199: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1272: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1273: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1278: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1280: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1280: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1280: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1287: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1292: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1294: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1303: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1308: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1338: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1340: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1340: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1341: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1343: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1346: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1347: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1347: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1349: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1350: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1351: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1352: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1354: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1356: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1357: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1362: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1363: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1364: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1366: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1372: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1376: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1377: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1380: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1391: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1434: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1447: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1450: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/Beauti.java:1473: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/beauti/guiutil/S11InitialSelection.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/Arrow.java:168: elipses ==> ellipses, eclipses, ellipsis data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/Arrow.java:173: elipse ==> ellipse, eclipse data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/Arrow.java:176: elipse ==> ellipse, eclipse data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/Arrow.java:176: elipse ==> ellipse, eclipse data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/Arrow.java:222: divsion ==> division data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectDialog.java:17: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectInputEditor.java:15: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectInputEditor.java:16: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:22: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:79: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BEASTObjectPanel.java:186: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/BooleanInputEditor.java:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/Document.java:1076: creat ==> create data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/Document.java:1548: ouputs ==> outputs data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/DoubleInputEditor.java:3: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/DoubleListInputEditor.java:21: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/DoubleListInputEditor.java:22: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/DoubleListInputEditor.java:23: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/EnumInputEditor.java:10: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditor.java:23: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditor.java:24: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditor.java:25: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:16: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:17: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:18: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:50: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:82: ingore ==> ignore data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/InputEditorFactory.java:333: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/IntegerInputEditor.java:3: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/IntegerListInputEditor.java:38: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/IntegerListInputEditor.java:39: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/IntegerListInputEditor.java:40: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ListInputEditor.java:26: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/LongInputEditor.java:3: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ModelBuilder.java:133: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ModelBuilder.java:451: extention ==> extension data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ModelBuilder.java:519: Extention ==> Extension data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/MyAction.java:18: definining ==> defining data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ParameterInputEditor.java:15: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ParameterInputEditor.java:16: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ParameterInputEditor.java:17: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/ParameterInputEditor.java:133: deLink ==> unlink data/beast2-mcmc-2.6.3+dfsg/src/beast/app/draw/StringInputEditor.java:3: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/seqgen/MergeDataWith.java:10: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/seqgen/MergeDataWith.java:27: occurrance ==> occurrence data/beast2-mcmc-2.6.3+dfsg/src/beast/app/seqgen/MergeDataWith.java:29: seccond ==> second data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/LogCombinerDialog.java:65: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/LogCombinerDialog.java:65: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/LogCombinerDialog.java:88: ouput ==> output data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/LogCombinerDialog.java:168: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/LogCombinerDialog.java:176: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/LogCombinerDialog.java:290: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/LogCombinerDialog.java:310: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/TableEditorStopper.java:12: whetehr ==> whether data/beast2-mcmc-2.6.3+dfsg/src/beast/app/tools/TableEditorStopper.java:38: transfered ==> transferred data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:39: Inconsistant ==> Inconsistent data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:122: invarient ==> invariant data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:123: invarient ==> invariant data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:123: occures ==> occurs data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:183: invarient ==> invariant data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:184: invarient ==> invariant data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:184: occures ==> occurs data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/ContourGenerator.java:836: intial ==> initial data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/FileDrop.java:886: anyting ==> anything data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/SnyderContour.java:11: Fortan ==> Fortran data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:34: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1106: CORDINATE ==> COORDINATE data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1106: cordinates ==> coordinates data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1162: CORDINATE ==> COORDINATE data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1201: CORDINATE ==> COORDINATE data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1570: ths ==> the, this data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1589: ths ==> the, this data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1608: ths ==> the, this data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeAnnotator.java:1610: ths ==> the, this data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeSetParser.java:339: qoutes ==> quotes data/beast2-mcmc-2.6.3+dfsg/src/beast/app/treeannotator/TreeSetParser.java:350: qoutes ==> quotes data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/ErrorLogHandler.java:30: encounted ==> encountered, encounter data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/FileDrop.java:884: anyting ==> anything data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils.java:4: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils.java:5: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils.java:142: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils.java:396: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils.java:403: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:130: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:180: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:314: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:317: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:334: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:338: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:366: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/app/util/Utils6.java:375: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/core/BEASTInterface.java:493: predecesor ==> predecessor data/beast2-mcmc-2.6.3+dfsg/src/beast/core/Input.java:486: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/core/Input.java:568: initilised ==> initialised, initialized data/beast2-mcmc-2.6.3+dfsg/src/beast/core/Input.java:849: expeted ==> expected data/beast2-mcmc-2.6.3+dfsg/src/beast/core/Logger.java:72: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/core/Logger.java:170: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/core/OperatorSchedule.java:250: accRate ==> accurate data/beast2-mcmc-2.6.3+dfsg/src/beast/core/OperatorSchedule.java:272: accRate ==> accurate data/beast2-mcmc-2.6.3+dfsg/src/beast/core/Param.java:14: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/core/StateNode.java:19: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/alignment/Alignment.java:94: unkown ==> unknown data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/alignment/AscertainedAlignment.java:6: Alignemnt ==> Alignment data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/alignment/FilteredAlignment.java:240: addjust ==> adjust data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/alignment/FilteredAlignment.java:264: addjust ==> adjust data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/branchratemodel/RateStatistic.java:45: coefficent ==> coefficient data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/datatype/StandardData.java:147: fro ==> for, from data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/datatype/StandardData.java:148: charcter ==> character data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/datatype/UserDataType.java:73: Invalide ==> Invalid data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/likelihood/LikelihoodCore.java:180: diagnosics ==> diagnostics data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/likelihood/ThreadedLikelihoodCore.java:138: diagnosics ==> diagnostics data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/likelihood/ThreadedTreeLikelihood.java:45: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/likelihood/ThreadedTreeLikelihood.java:45: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/likelihood/ThreadedTreeLikelihood.java:81: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/likelihood/ThreadedTreeLikelihood.java:82: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/likelihood/ThreadedTreeLikelihood.java:247: cummulative ==> cumulative data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/operators/DeltaExchangeOperator.java:55: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/operators/IntUniformOperator.java:20: depracated ==> deprecated data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/operators/NodeReheight.java:44: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/operators/NodeReheight.java:45: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/operators/NodeReheight.java:104: Inconsisten ==> Inconsistent data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/sitemodel/SiteModel.java:122: bewteen ==> between data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/speciation/CalibratedBirthDeathModel.java:165: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/speciation/CalibratedBirthDeathModel.java:213: thier ==> their data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/speciation/CalibratedYuleModel.java:157: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/speciation/CalibratedYuleModel.java:205: thier ==> their data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/speciation/GeneTreeForSpeciesTreeDistribution.java:81: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/speciation/SpeciesTreePrior.java:95: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/speciation/StarBeastStartState.java:68: initialse ==> initialise, initialize data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/substitutionmodel/BinaryCovarion.java:78: impementation ==> implementation data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/substitutionmodel/Dayhoff.java:10: Structur ==> Structure data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/substitutionmodel/WAG.java:253: Ser ==> Set data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/substitutionmodel/WAG.java:442: Ser ==> Set data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/RandomTree.java:238: tHi ==> the, this data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/RandomTree.java:240: tHi ==> the, this data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/RandomTree.java:241: tHi ==> the, this data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/TreeUtils.java:318: fo ==> of, for data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/TreeUtils.java:332: fo ==> of, for data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/BayesianSkyline.java:301: agains ==> against, again data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/CompoundPopulationFunction.java:500: nd ==> and, 2nd data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/CompoundPopulationFunction.java:502: nd ==> and, 2nd data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/CompoundPopulationFunction.java:503: nd ==> and, 2nd data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/CompoundPopulationFunction.java:503: nd ==> and, 2nd data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/CompoundPopulationFunction.java:504: nd ==> and, 2nd data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/CompoundPopulationFunction.java:520: nd ==> and, 2nd data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/ConstantPopulation.java:95: unecessary ==> unnecessary data/beast2-mcmc-2.6.3+dfsg/src/beast/evolution/tree/coalescent/ScaledPopulationFunction.java:24: facor ==> favor, faker data/beast2-mcmc-2.6.3+dfsg/src/beast/math/distributions/MRCAPrior.java:379: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/math/distributions/Normal.java:20: precission ==> precision, percussion, precession data/beast2-mcmc-2.6.3+dfsg/src/beast/math/statistic/RPNcalculator.java:114: wront ==> wrong data/beast2-mcmc-2.6.3+dfsg/src/beast/util/HeapSort.java:21: refering ==> referring data/beast2-mcmc-2.6.3+dfsg/src/beast/util/HeapSort.java:129: ingoring ==> ignoring data/beast2-mcmc-2.6.3+dfsg/src/beast/util/JSONParser.java:232: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/JSONParser.java:300: intialize ==> initialize data/beast2-mcmc-2.6.3+dfsg/src/beast/util/JSONParser.java:898: intialize ==> initialize data/beast2-mcmc-2.6.3+dfsg/src/beast/util/JSONProducer.java:417: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/MersenneTwisterFast.java:141: inforce ==> enforce data/beast2-mcmc-2.6.3+dfsg/src/beast/util/MersenneTwisterFast.java:144: curernt ==> current data/beast2-mcmc-2.6.3+dfsg/src/beast/util/MersenneTwisterFast.java:174: Initalize ==> Initialize data/beast2-mcmc-2.6.3+dfsg/src/beast/util/NexusParser.java:174: begining ==> beginning data/beast2-mcmc-2.6.3+dfsg/src/beast/util/NexusParser.java:206: begining ==> beginning data/beast2-mcmc-2.6.3+dfsg/src/beast/util/NexusParser.java:374: intput ==> input data/beast2-mcmc-2.6.3+dfsg/src/beast/util/NexusParser.java:408: intput ==> input data/beast2-mcmc-2.6.3+dfsg/src/beast/util/NexusParser.java:1112: wont ==> won't data/beast2-mcmc-2.6.3+dfsg/src/beast/util/NexusParser.java:1313: Unknwon ==> Unknown data/beast2-mcmc-2.6.3+dfsg/src/beast/util/Package.java:9: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/Package.java:14: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:39: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:42: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:52: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:64: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:64: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:69: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:70: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:72: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageDependency.java:73: atLeast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:72: ons ==> owns data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:73: ons ==> owns data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:74: ons ==> owns data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:77: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:144: ons ==> owns data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:254: atleast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:350: atleast ==> at least data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:463: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:490: pacakge ==> package data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:491: bussy ==> busy data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:631: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:1969: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:2107: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/PackageManager.java:2110: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/XMLParser.java:28: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/XMLParser.java:29: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/XMLParser.java:452: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/XMLParser.java:522: intialize ==> initialize data/beast2-mcmc-2.6.3+dfsg/src/beast/util/XMLParser.java:944: intialize ==> initialize data/beast2-mcmc-2.6.3+dfsg/src/beast/util/XMLProducer.java:86: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/TreeParser.java:84: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/TreeParser.java:154: initalising ==> initialising data/beast2-mcmc-2.6.3+dfsg/src/beast/util/TreeParser.java:154: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/beast/util/treeparser/NewickLexer.java:148: 2ST ==> 2ND data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/analysis/solvers/MullerSolver.java:33: arithmetics ==> arithmetic data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/analysis/solvers/UnivariateRealSolverImpl.java:264: enpoints ==> endpoints data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/CauchyDistributionImpl.java:99: evaluted ==> evaluated data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/HasDensity.java:42: specifed ==> specified data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/IntegerDistribution.java:67: postive ==> positive data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/NormalDistributionImpl.java:209: evaluted ==> evaluated data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/PoissonDistributionImpl.java:92: probabilites ==> probabilities data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/PoissonDistributionImpl.java:93: probabilites ==> probabilities data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/PoissonDistributionImpl.java:106: probabilites ==> probabilities data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/PoissonDistributionImpl.java:118: probabilites ==> probabilities data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/distribution/TDistributionImpl.java:137: evaluted ==> evaluated data/beast2-mcmc-2.6.3+dfsg/src/org/apache/commons/math/util/MathUtils.java:1106: sould ==> could, should, sold data/beast2-mcmc-2.6.3+dfsg/src/org/json/JSONObject.java:76: overrideable ==> overridable data/beast2-mcmc-2.6.3+dfsg/src/org/json/JSONStringer.java:57: overrideable ==> overridable data/beast2-mcmc-2.6.3+dfsg/src/org/json/JSONTokener.java:58: overrideable ==> overridable data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiTest.java:8: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiTest.java:8: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiTest.java:9: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiTest.java:22: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiTest.java:38: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiTest.java:59: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiTest.java:142: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiSubTemplateTest.java:5: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiSubTemplateTest.java:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiSubTemplateTest.java:58: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiSubTemplateTest.java:77: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiSubTemplateTest.java:78: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiSubTemplateTest.java:81: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/BeautiSubTemplateTest.java:82: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:31: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:31: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:32: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:51: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:57: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:57: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:66: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:66: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:67: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:75: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:75: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:75: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:76: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:290: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:324: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:355: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiBase.java:356: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:277: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:289: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:303: doubleClick ==> double-click data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:400: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:435: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:468: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiDivergenceDatingTest.java:493: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:34: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:157: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:173: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:177: Seting ==> Setting data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:185: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:202: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:221: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:245: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:280: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiRateTutorialTest.java:293: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiSimpleTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiSimpleTest.java:58: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiSimpleTest.java:91: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiSimpleTest.java:108: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiSimpleTest.java:112: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:21: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:33: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:46: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:59: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:77: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:84: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:86: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:88: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:100: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/BeautiStarBeastTest.java:113: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/CloneTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/FixedMeanRateTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/FixedMeanRateTest.java:42: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/FixedMeanRateTest.java:66: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/FixedMeanRateTest.java:80: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/LinkUnlinkTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/LinkUnlinkTest.java:542: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/LinkUnlinkTest.java:543: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/SimpleClockModelTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/beauti/SimpleTreePriorTest.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/app/tools/LogCombinerTest.java:10: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/beast2vs1/trace/LogAnalyser.java:55: availble ==> available data/beast2-mcmc-2.6.3+dfsg/src/test/beast/beast2vs1/trace/LogAnalyser.java:57: availble ==> available data/beast2-mcmc-2.6.3+dfsg/src/test/beast/beast2vs1/tutorials/RateTutorialTest.java:14: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/core/BEASTInterfaceTest.java:21: impements ==> implements data/beast2-mcmc-2.6.3+dfsg/src/test/beast/core/BEASTInterfaceTest.java:106: impements ==> implements data/beast2-mcmc-2.6.3+dfsg/src/test/beast/core/InputTest.java:11: impements ==> implements data/beast2-mcmc-2.6.3+dfsg/src/test/beast/evolution/datatype/DataTypeDeEncodeTest.java:34: dAa ==> data data/beast2-mcmc-2.6.3+dfsg/src/test/beast/evolution/datatype/DataTypeDeEncodeTest.java:46: dAa ==> data data/beast2-mcmc-2.6.3+dfsg/src/test/beast/evolution/operator/UniformIntegerOperatorTest.java:23: vaules ==> values data/beast2-mcmc-2.6.3+dfsg/src/test/beast/evolution/operator/UniformIntegerOperatorTest.java:58: vaules ==> values data/beast2-mcmc-2.6.3+dfsg/src/test/beast/evolution/tree/TreeAnnotatorTest.java:13: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/src/test/beast/integration/InputTypeTest.java:59: constructure ==> constructor data/beast2-mcmc-2.6.3+dfsg/src/test/beast/integration/InputTypeTest.java:103: arrray ==> array data/beast2-mcmc-2.6.3+dfsg/src/test/beast/util/JSONTest.java:10: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/ClockModels.xml:3: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/ParametricDistributions.xml:2: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/Standard.xml:2: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/Standard.xml:5: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/Standard.xml:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/Standard.xml:102: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/Standard.xml:240: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/Standard.xml:244: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/StarBeast.xml:2: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/StarBeast.xml:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/StarBeast.xml:7: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/StarBeast.xml:102: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/SubstModels.xml:2: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/SubstModels.xml:28: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/TreePriors.xml:2: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/templates/TreePriors.xml:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/beast2-mcmc.manifest:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/rules:31: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/rules:33: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/bin/beast2-mcmc:8: explicitely ==> explicitly data/beast2-mcmc-2.6.3+dfsg/debian/bin/beauti2:8: explicitely ==> explicitly data/beast2-mcmc-2.6.3+dfsg/debian/bin/beauti2:49: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/bin/treeannotator2:8: explicitely ==> explicitly data/beast2-mcmc-2.6.3+dfsg/debian/mans/beauti2.1:21: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/debian/mans/beauti2.1:24: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_jsign_from_build.patch:22: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_jsign_from_build.patch:115: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:7: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:7: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:8: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:8: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:9: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:15: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:17: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:28: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/debian/patches/remove_mac_only_code.patch:34: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/debian/tests/run-build-tests:110: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:88: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:167: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:226: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:244: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:247: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:261: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:277: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:302: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:351: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:369: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:494: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:545: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:563: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:687: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:709: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:741: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:742: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:755: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:780: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:812: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:813: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:902: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:907: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:907: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:908: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:911: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:915: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1135: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1140: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1140: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1141: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1144: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1148: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1154: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1155: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1156: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1402: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1406: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1406: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1413: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1426: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1427: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1427: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1429: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1430: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1476: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1477: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1477: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1479: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/fix_classpath_in_build_xml.patch/build.xml:1480: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:88: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:167: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:226: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:244: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:247: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:261: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:277: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:302: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:351: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:369: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:494: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:545: BEAUTi ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:563: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:687: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:709: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:741: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:742: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:755: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:780: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:812: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:813: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:902: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:907: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:907: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:908: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:911: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:915: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1135: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1140: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1140: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1141: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1144: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1148: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1154: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1155: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1156: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1402: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1406: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1406: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1413: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1426: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1427: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1427: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1429: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1430: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1476: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1477: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1477: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1479: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_appbundler.patch/build.xml:1480: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/antlr-compatibility.patch/src/beast/util/TreeParser.java:84: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/antlr-compatibility.patch/src/beast/util/TreeParser.java:154: initalising ==> initialising data/beast2-mcmc-2.6.3+dfsg/.pc/antlr-compatibility.patch/src/beast/util/TreeParser.java:154: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/antlr-compatibility.patch/src/beast/util/treeparser/NewickLexer.java:149: 2ST ==> 2ND data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:1: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:6: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:7: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:51: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:53: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:107: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:112: Beauti ==> Beauty 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data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:1448: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:1451: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_mac_only_code.patch/src/beast/app/beauti/Beauti.java:1474: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:88: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:167: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:226: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:244: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:247: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:261: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:277: BEAUti 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data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:755: BEAUTI ==> BEAUTY data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:780: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:812: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:813: manaully ==> manually data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:899: BEAUti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:904: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:904: Beauti ==> Beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:905: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:908: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/remove_jsign_from_build.patch/build.xml:912: BEAUti ==> beauty 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data/beast2-mcmc-2.6.3+dfsg/.pc/handling_minor_issues_in_tests.patch/src/test/beast/app/BeautiSubTemplateTest.java:228: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/handling_minor_issues_in_tests.patch/src/test/beast/app/BeautiSubTemplateTest.java:229: beauti ==> beauty data/beast2-mcmc-2.6.3+dfsg/.pc/handling_minor_issues_in_tests.patch/src/test/beast/evolution/tree/TreeAnnotatorTest.java:13: beauti ==> beauty