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data/phyutility-2.7.3+dfsg/src/jade/data/TransitionPenaltyTable.java: ASCII text, with CRLF line terminators data/phyutility-2.7.3+dfsg/src/jade/lib/compile.sh: ASCII text data/phyutility-2.7.3+dfsg/src/jade/lib/instr: ASCII text data/phyutility-2.7.3+dfsg/src/jade/lib/jade_reconstruct_area_PJNI.c: C source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/lib/jade_reconstruct_area_PJNI.h: C source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/math/AP_Basic.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/math/AP_Praxis.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/math/AP_praxis_method.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/math/BetaDistribution.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/math/ContinuedFraction.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/math/ExponentialDistribution.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/math/GammaDistribution.java: Java source, ASCII text 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data/phyutility-2.7.3+dfsg/src/jade/math/fRan.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/AncSplit.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/Area.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/BayesChain.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/BayesianMarginalRangeReconstructor.java: Java source, ASCII text, with very long lines data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/BayesianMarginalRangeReconstructorMult.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/BranchSegment.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/JointRangeReconstructor.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/MarginalRangeReconstructor.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/MatrixExponential.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/P.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/PJAMA.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/PJNI.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/Q.java: ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/RangeReconstructionOptimizer.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/RangeReconstructionOptimizerDispersal.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/RangeReconstructionOptimizerLocalExtinction.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/RangeReconstructionOptimizerMult.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jade/reconstruct/area/RangeReconstructionOptimizerMultDispersal.java: Java source, ASCII text 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data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/package.html: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/AminoAcidScores.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum45.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum50.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum55.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum60.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum62.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum65.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum70.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum75.java: ASCII text data/phyutility-2.7.3+dfsg/src/jebl/evolution/align/scores/Blosum80.java: ASCII text 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data/phyutility-2.7.3+dfsg/src/jebl/util/FixedBitSet.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jebl/util/NumberFormatter.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jebl/util/ProgressListener.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/jebl/util/Utils.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/app/Arguments.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/app/Utils.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/components/JVerticalLabel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/components/RealNumberField.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/components/WholeNumberField.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/console/ConsoleApplication.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/console/ConsoleFrame.java: Java source, 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data/phyutility-2.7.3+dfsg/src/org/virion/jam/controlpanels/ControlsSettings.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/DemoApplication.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/DemoFrame.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/DemoMenuBarFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/images/filterBackground.png: PNG image data, 80 x 25, 8-bit/color RGB, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/images/find.png: PNG image data, 20 x 14, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/images/infoTool.png: PNG image data, 32 x 32, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/images/prefsAdvanced.png: PNG image data, 32 x 32, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/demo/images/prefsClipboard.png: PNG image data, 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data/phyutility-2.7.3+dfsg/src/org/virion/jam/disclosure/DisclosurePanel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/disclosure/images/disclosureDownNormal.png: PNG image data, 13 x 13, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/disclosure/images/disclosureDownPressed.png: PNG image data, 13 x 13, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/disclosure/images/disclosureRightDown.png: PNG image data, 13 x 13, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/disclosure/images/disclosureRightNormal.png: PNG image data, 13 x 13, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/disclosure/images/disclosureRightPressed.png: PNG image data, 13 x 13, 8-bit/color RGBA, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/disclosure/images/titleBackground.png: PNG image data, 80 x 25, 8-bit/color RGB, non-interlaced data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/AboutBox.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/AbstractFrame.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/Application.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/AuxilaryFrame.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/Command.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/DefaultEditMenuFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/DefaultFileMenuFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/DefaultHelpMenuFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/DefaultMenuBarFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/DocumentFrame.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/DocumentFrameFactory.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/Exportable.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/MenuBarFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/MenuFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/MultiDocApplication.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/MultiDocMenuBarFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/RecentFileList.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/SingleDocApplication.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/framework/SingleDocMenuBarFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/html/HTMLViewer.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/html/SimpleLinkListener.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/layouts/CompassLayout.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/mac/MacFileMenuFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/mac/MacHelpMenuFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/mac/MacWindowMenuFactory.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/mac/Utils.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/maconly/OSXAdapter.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/ActionPanel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/AddRemovePanel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/OptionsPanel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/RuleModel.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/RulesPanel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/SearchPanel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/SearchPanelListener.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/StatusBar.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/StatusListener.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/StatusPanel.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/StatusProvider.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/panels/images/action/actionButton.png: PNG image data, 28 x 22, 8-bit/color RGBA, non-interlaced 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data/phyutility-2.7.3+dfsg/src/org/virion/jam/table/TableRenderer.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/table/WholeNumberCellEditor.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/toolbar/GenericToolbarItem.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/toolbar/Toolbar.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/toolbar/ToolbarAction.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/toolbar/ToolbarButton.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/toolbar/ToolbarItem.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/toolbar/ToolbarOptions.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/BrowserLauncher.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/IconUtils.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/JExceptionDialog.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/ListItemView.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/LongTask.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/LongTaskMonitor.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/PrintUtilities.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/SimpleListener.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/SimpleListenerManager.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/SimpleLongTask.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/SwingWorker.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/TaskListener.java: ASCII text data/phyutility-2.7.3+dfsg/src/org/virion/jam/util/Utils.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/AttributeList.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/Attributes.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ContentHandler.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/DTDHandler.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/DocumentHandler.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/EntityResolver.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ErrorHandler.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/HandlerBase.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/InputSource.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/Locator.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/Parser.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/SAXException.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/SAXNotRecognizedException.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/SAXNotSupportedException.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/SAXParseException.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/XMLFilter.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/XMLReader.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/Attributes2.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/Attributes2Impl.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/DeclHandler.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/DefaultHandler2.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/EntityResolver2.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/LexicalHandler.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/Locator2.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/Locator2Impl.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/ext/package.html: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/AttributeListImpl.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/AttributesImpl.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/DefaultHandler.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/LocatorImpl.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/NamespaceSupport.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/NewInstance.java: C++ source, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/ParserAdapter.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/ParserFactory.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/XMLFilterImpl.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/XMLReaderAdapter.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/XMLReaderFactory.java: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/helpers/package.html: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/org/xml/sax/package.html: HTML document, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/concat/Concat.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/consensus/Consensus.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/drb/WwdEmbedded.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/drb/WwdUtils.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/jebl2jade/NexusToJade.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/leafstability/Calculator.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/leafstability/Runner.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/lineagemovement/Main.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/mainrunner/Main.java: data data/phyutility-2.7.3+dfsg/src/phyutility/mainrunner/TestFuncs.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/mainrunner/Utils.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/ncbi/EFetchContentHandler.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/ncbi/ESearchContentHandler.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/ncbi/Einfo.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/pruner/Pruner.java: Java source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/treesupport/Runner.java: C source, ASCII text data/phyutility-2.7.3+dfsg/src/phyutility/trimsites/TrimSites.java: C source, ASCII text data/phyutility-2.7.3+dfsg/debian/bin/phyutility: POSIX shell script, ASCII text executable data/phyutility-2.7.3+dfsg/debian/changelog: ASCII text data/phyutility-2.7.3+dfsg/debian/control: ASCII text data/phyutility-2.7.3+dfsg/debian/copyright: UTF-8 Unicode text data/phyutility-2.7.3+dfsg/debian/install: ASCII text data/phyutility-2.7.3+dfsg/debian/jlibs: ASCII text data/phyutility-2.7.3+dfsg/debian/patches/series: ASCII text data/phyutility-2.7.3+dfsg/debian/patches/stick_to_java_8_until_xml.sax_is_removed.patch: unified diff output, ASCII text data/phyutility-2.7.3+dfsg/debian/phyutility.1: troff or preprocessor input, ASCII text data/phyutility-2.7.3+dfsg/debian/phyutility.manpages: ASCII text data/phyutility-2.7.3+dfsg/debian/rules: a /usr/bin/make -f script, ASCII text executable data/phyutility-2.7.3+dfsg/debian/salsa-ci.yml: ASCII text data/phyutility-2.7.3+dfsg/debian/source/format: ASCII text data/phyutility-2.7.3+dfsg/debian/upstream/metadata: ASCII text data/phyutility-2.7.3+dfsg/debian/watch: ASCII text data/phyutility-2.7.3+dfsg/.pc/.version: ASCII text data/phyutility-2.7.3+dfsg/.pc/.quilt_patches: ASCII text data/phyutility-2.7.3+dfsg/.pc/.quilt_series: ASCII text data/phyutility-2.7.3+dfsg/.pc/applied-patches: ASCII text data/phyutility-2.7.3+dfsg/.pc/stick_to_java_8_until_xml.sax_is_removed.patch/build.xml: ASCII text data/phyutility-2.7.3+dfsg/build.xml: ASCII text