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new version of muscle 3.8.31
[jabaws.git] / binaries / src / muscle / muscle.vcproj
diff --git a/binaries/src/muscle/muscle.vcproj b/binaries/src/muscle/muscle.vcproj
new file mode 100644 (file)
index 0000000..226dac2
--- /dev/null
+++ b/binaries/src/muscle/muscle.vcproj
@@ -0,0 +1,922 @@
+<?xml version="1.0" encoding="Windows-1252"?>\r
+<VisualStudioProject\r
+       ProjectType="Visual C++"\r
+       Version="9.00"\r
+       Name="muscle"\r
+       ProjectGUID="{57FBAB99-B961-4B38-B846-CA26D63384F2}"\r
+       RootNamespace="muscle3.6"\r
+       Keyword="Win32Proj"\r
+       TargetFrameworkVersion="131072"\r
+       >\r
+       <Platforms>\r
+               <Platform\r
+                       Name="Win32"\r
+               />\r
+       </Platforms>\r
+       <ToolFiles>\r
+       </ToolFiles>\r
+       <Configurations>\r
+               <Configuration\r
+                       Name="Debug|Win32"\r
+                       OutputDirectory="Debug"\r
+                       IntermediateDirectory="Debug"\r
+                       ConfigurationType="1"\r
+                       InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC70.vsprops"\r
+                       CharacterSet="2"\r
+                       >\r
+                       <Tool\r
+                               Name="VCPreBuildEventTool"\r
+                               Description="SVN version"\r
+                               CommandLine="c:\cygwin\bin\bash c:/cygwin/bin/svnver"\r
+                       />\r
+                       <Tool\r
+                               Name="VCCustomBuildTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCXMLDataGeneratorTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCWebServiceProxyGeneratorTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCMIDLTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCCLCompilerTool"\r
+                               Optimization="0"\r
+                               PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE;_WIN32_WINNT=0x0400"\r
+                               MinimalRebuild="true"\r
+                               BasicRuntimeChecks="3"\r
+                               RuntimeLibrary="1"\r
+                               UsePrecompiledHeader="0"\r
+                               BrowseInformation="1"\r
+                               WarningLevel="3"\r
+                               Detect64BitPortabilityProblems="false"\r
+                               DebugInformationFormat="4"\r
+                       />\r
+                       <Tool\r
+                               Name="VCManagedResourceCompilerTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCResourceCompilerTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCPreLinkEventTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCLinkerTool"\r
+                               AdditionalDependencies="psapi.lib user32.lib"\r
+                               OutputFile="$(OutDir)/muscle.exe"\r
+                               LinkIncremental="2"\r
+                               GenerateDebugInformation="true"\r
+                               ProgramDatabaseFile="$(OutDir)/muscle.pdb"\r
+                               SubSystem="1"\r
+                               RandomizedBaseAddress="1"\r
+                               DataExecutionPrevention="0"\r
+                               TargetMachine="1"\r
+                       />\r
+                       <Tool\r
+                               Name="VCALinkTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCManifestTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCXDCMakeTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCBscMakeTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCFxCopTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCAppVerifierTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCPostBuildEventTool"\r
+                       />\r
+               </Configuration>\r
+               <Configuration\r
+                       Name="Release|Win32"\r
+                       OutputDirectory="Release"\r
+                       IntermediateDirectory="Release"\r
+                       ConfigurationType="1"\r
+                       InheritedPropertySheets="$(VCInstallDir)VCProjectDefaults\UpgradeFromVC70.vsprops"\r
+                       CharacterSet="2"\r
+                       >\r
+                       <Tool\r
+                               Name="VCPreBuildEventTool"\r
+                               Description="SVN version"\r
+                               CommandLine="c:\cygwin\bin\bash c:/cygwin/bin/svnver"\r
+                       />\r
+                       <Tool\r
+                               Name="VCCustomBuildTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCXMLDataGeneratorTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCWebServiceProxyGeneratorTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCMIDLTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCCLCompilerTool"\r
+                               Optimization="2"\r
+                               InlineFunctionExpansion="1"\r
+                               OmitFramePointers="true"\r
+                               PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE;_WIN32_WINNT=0x0400"\r
+                               StringPooling="true"\r
+                               RuntimeLibrary="0"\r
+                               EnableFunctionLevelLinking="true"\r
+                               ForceConformanceInForLoopScope="true"\r
+                               UsePrecompiledHeader="0"\r
+                               BrowseInformation="1"\r
+                               WarningLevel="3"\r
+                               Detect64BitPortabilityProblems="false"\r
+                               DebugInformationFormat="3"\r
+                       />\r
+                       <Tool\r
+                               Name="VCManagedResourceCompilerTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCResourceCompilerTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCPreLinkEventTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCLinkerTool"\r
+                               AdditionalDependencies="psapi.lib user32.lib"\r
+                               OutputFile="$(OutDir)/muscle.exe"\r
+                               LinkIncremental="1"\r
+                               GenerateDebugInformation="true"\r
+                               SubSystem="1"\r
+                               OptimizeReferences="2"\r
+                               EnableCOMDATFolding="2"\r
+                               RandomizedBaseAddress="1"\r
+                               DataExecutionPrevention="0"\r
+                               TargetMachine="1"\r
+                       />\r
+                       <Tool\r
+                               Name="VCALinkTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCManifestTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCXDCMakeTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCBscMakeTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCFxCopTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCAppVerifierTool"\r
+                       />\r
+                       <Tool\r
+                               Name="VCPostBuildEventTool"\r
+                       />\r
+               </Configuration>\r
+       </Configurations>\r
+       <References>\r
+       </References>\r
+       <Files>\r
+               <Filter\r
+                       Name="Source Files"\r
+                       Filter="cpp;c;cxx;def;odl;idl;hpj;bat;asm"\r
+                       >\r
+                       <File\r
+                               RelativePath="aligngivenpath.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="aligngivenpathsw.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="aligntwomsas.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="aligntwoprofs.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="aln.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="alpha.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="anchors.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="bittraceback.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath=".\blosum62.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="blosumla.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="clust.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="cluster.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="clwwt.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="color.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="cons.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="diaglist.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="diffobjscore.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="diffpaths.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="difftrees.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="difftreese.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="distcalc.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="distfunc.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="distpwkimura.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="domuscle.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="dosp.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="dpreglist.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="drawtree.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="edgelist.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="enumopts.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="enumtostr.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="estring.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fasta.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fasta2.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastclust.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastdist.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastdistjones.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastdistkbit.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastdistkmer.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastdistmafft.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastdistnuc.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="fastscorepath2.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="finddiags.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="finddiagsn.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalign.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalign352.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbaligndiag.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalignle.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalignsimple.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalignsp.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalignspn.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalignss.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="glbalndimer.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="globals.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="globalslinux.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath=".\globalsosx.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath=".\globalsother.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="globalswin32.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="gonnet.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="henikoffweight.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="henikoffweightpb.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="html.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="hydro.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="intmath.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="local.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="main.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="makerootmsa.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="makerootmsab.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath=".\maketree.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="mhack.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="mpam200.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="msa.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="msa2.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="msadistkimura.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="msf.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="muscle.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="muscleout.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="nucmx.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="nwdasimple.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="nwdasimple2.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="nwdasmall.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="nwrec.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="nwsmall.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="objscore.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="objscore2.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="objscoreda.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="onexception.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="options.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="outweights.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="pam200mafft.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="params.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="phy.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="phy2.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="phy3.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="phy4.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="phyfromclust.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="phyfromfile.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="physeq.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="phytofile.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="posgap.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="ppscore.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="profdb.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="profile.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="profilefrommsa.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="progalign.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="progress.cpp"\r
+                               >\r
+                       </File>\r
+                       <File\r
+                               RelativePath="progressivealign.cpp"\r
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