]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
1.18.1
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 2f3cc5520b1b3454081b9db51fe4d75662070c18..6bc5e178281bbdc2a993986280a9a366864c07eb 100644 (file)
@@ -7,12 +7,18 @@
        objects = {
 
 /* Begin PBXBuildFile section */
+               7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
                8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; };
                A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; };
                A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
                A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
+               A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB15E130B04A2001E7287 /* anosimcommand.cpp */; };
                A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; };
                A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
+               A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
+               A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */; };
+               A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
+               A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; };
                A7E9B88112D37EC400DA6239 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B64F12D37EC300DA6239 /* ace.cpp */; };
                A7E9B88212D37EC400DA6239 /* aligncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65112D37EC300DA6239 /* aligncommand.cpp */; };
                A7E9B88312D37EC400DA6239 /* alignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B65312D37EC300DA6239 /* alignment.cpp */; };
@@ -41,7 +47,6 @@
                A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */; };
                A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */; };
                A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */; };
-               A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */; };
                A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */; };
                A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */; };
                A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */; };
                A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */; };
                A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */; };
                A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */; };
-               A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70C12D37EC400DA6239 /* globaldata.cpp */; };
                A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */; };
                A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */; };
                A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B71212D37EC400DA6239 /* gower.cpp */; };
                A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B212D37EC400DA6239 /* readcluster.cpp */; };
                A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */; };
                A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */; };
-               A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7B912D37EC400DA6239 /* readotu.cpp */; };
                A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */; };
                A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */; };
                A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7BF12D37EC400DA6239 /* readtree.cpp */; };
                A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87C12D37EC400DA6239 /* weighted.cpp */; };
                A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */; };
                A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B87F12D37EC400DA6239 /* whittaker.cpp */; };
+               A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FA10011302E096003860FE /* mantelcommand.cpp */; };
                A7FC480E12D788F20055BC5C /* linearalgebra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC480D12D788F20055BC5C /* linearalgebra.cpp */; };
                A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; };
+               A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */; };
+               A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */; };
 /* End PBXBuildFile section */
 
 /* Begin PBXCopyFilesBuildPhase section */
 /* End PBXCopyFilesBuildPhase section */
 
 /* Begin PBXFileReference section */
+               7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
+               7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
                A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
                A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
                A713EBEB12DC7C5E000092AC /* nmdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nmdscommand.h; sourceTree = "<group>"; };
                A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nmdscommand.cpp; sourceTree = "<group>"; };
+               A71CB15E130B04A2001E7287 /* anosimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = anosimcommand.cpp; sourceTree = "<group>"; };
+               A71CB15F130B04A2001E7287 /* anosimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = anosimcommand.h; sourceTree = "<group>"; };
                A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergegroupscommand.h; sourceTree = "<group>"; };
                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergegroupscommand.cpp; sourceTree = "<group>"; };
                A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = "<group>"; };
                A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = "<group>"; };
+               A75790571301749D00A30DAB /* homovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = homovacommand.h; sourceTree = "<group>"; };
+               A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = "<group>"; };
+               A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcommandinfocommand.h; sourceTree = "<group>"; };
+               A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcommandinfocommand.cpp; sourceTree = "<group>"; };
+               A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
+               A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
+               A7A61F1A130035C800E05B6B /* LICENSE */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = text; path = LICENSE; sourceTree = "<group>"; };
+               A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
+               A7A61F2C130062E000E05B6B /* amovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = amovacommand.cpp; sourceTree = "<group>"; };
+               A7AACFBA132FE008003D6C4D /* currentfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = currentfile.h; sourceTree = "<group>"; };
+               A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
                A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
                A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = "<group>"; };
                A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerarealigner.cpp; sourceTree = "<group>"; };
                A7E9B68512D37EC400DA6239 /* chimerarealigner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerarealigner.h; sourceTree = "<group>"; };
-               A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = "<group>"; };
-               A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = "<group>"; };
                A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayer.cpp; sourceTree = "<group>"; };
                A7E9B68912D37EC400DA6239 /* chimeraslayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayer.h; sourceTree = "<group>"; };
                A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = "<group>"; };
                A7E9B70912D37EC400DA6239 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = "<group>"; };
                A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = "<group>"; };
                A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = "<group>"; };
-               A7E9B70C12D37EC400DA6239 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B70D12D37EC400DA6239 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = SOURCE_ROOT; };
                A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = "<group>"; };
                A7E9B70F12D37EC400DA6239 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = "<group>"; };
                A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; };
                A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
                A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
                A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
-               A7E9B7B912D37EC400DA6239 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = "<group>"; };
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                A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
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                A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
                A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; };
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                A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
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+               A7FA10011302E096003860FE /* mantelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mantelcommand.cpp; sourceTree = "<group>"; };
                A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = "<group>"; };
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                A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = "<group>"; };
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+               A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcurrentcommand.cpp; sourceTree = "<group>"; };
+               A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setcurrentcommand.h; sourceTree = "<group>"; };
+               A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setcurrentcommand.cpp; sourceTree = "<group>"; };
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 /* End PBXFileReference section */
 
                08FB7795FE84155DC02AAC07 /* Source */ = {
                        isa = PBXGroup;
                        children = (
+                               A7A61F1A130035C800E05B6B /* LICENSE */,
                                A70332B512D3A13400761E33 /* makefile */,
                                A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */,
                                A7E9BA4F12D398D700DA6239 /* clearcut */,
                                A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */,
                                A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */,
                                A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */,
+                               A7DAAFA3133A254E003956EB /* commandparameter.h */,
                                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
                                A7E9BA4212D3960D00DA6239 /* containers */,
+                               A7AACFBA132FE008003D6C4D /* currentfile.h */,
                                A7E9B6C912D37EC400DA6239 /* display.h */,
                                A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */,
                                A7E9B6D212D37EC400DA6239 /* dlibshuff.h */,
                                A7E9B6DB12D37EC400DA6239 /* engine.hpp */,
                                A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */,
                                A7E9B6E112D37EC400DA6239 /* fileoutput.h */,
-                               A7E9B70C12D37EC400DA6239 /* globaldata.cpp */,
-                               A7E9B70D12D37EC400DA6239 /* globaldata.hpp */,
                                A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */,
                                A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */,
                                A7E9B71812D37EC400DA6239 /* hcluster.cpp */,
                                A7E9B75C12D37EC400DA6239 /* mothur.h */,
                                A7E9B75D12D37EC400DA6239 /* mothurout.cpp */,
                                A7E9B75E12D37EC400DA6239 /* mothurout.h */,
+                               A7E9B76112D37EC400DA6239 /* nast.cpp */,
+                               A7E9B76212D37EC400DA6239 /* nast.hpp */,
+                               A7E9B76312D37EC400DA6239 /* nastreport.cpp */,
+                               A7E9B76412D37EC400DA6239 /* nastreport.hpp */,
+                               A7E9B76712D37EC400DA6239 /* noalign.cpp */,
+                               A7E9B76812D37EC400DA6239 /* noalign.hpp */,
                                A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */,
                                A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */,
                                A7E9B77012D37EC400DA6239 /* observable.h */,
                                A7E9B7A912D37EC400DA6239 /* rarefact.cpp */,
                                A7E9B7AA12D37EC400DA6239 /* rarefact.h */,
                                A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */,
+                               7E6BE10812F710D8007ADDBE /* refchimeratest.h */,
+                               7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */,
                                A7E9BA5312D39A5E00DA6239 /* read */,
-                               A7E9B76112D37EC400DA6239 /* nast.cpp */,
-                               A7E9B76212D37EC400DA6239 /* nast.hpp */,
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-                               A7E9B76412D37EC400DA6239 /* nastreport.hpp */,
-                               A7E9B76712D37EC400DA6239 /* noalign.cpp */,
-                               A7E9B76812D37EC400DA6239 /* noalign.hpp */,
                                A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */,
                                A7E9B82412D37EC400DA6239 /* sharedutilities.h */,
                                A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
                                A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
-                               A7E9B83112D37EC400DA6239 /* slibshuff.h */,
                                A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
+                               A7E9B83112D37EC400DA6239 /* slibshuff.h */,
                                A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
                                A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
                                A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
                        isa = PBXGroup;
                        children = (
                                A7E9B6AE12D37EC400DA6239 /* command.hpp */,
-                               A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
                                A7E9B65212D37EC300DA6239 /* aligncommand.h */,
-                               A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
+                               A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
+                               A7A61F2B130062E000E05B6B /* amovacommand.h */,
+                               A7A61F2C130062E000E05B6B /* amovacommand.cpp */,
+                               A71CB15F130B04A2001E7287 /* anosimcommand.h */,
+                               A71CB15E130B04A2001E7287 /* anosimcommand.cpp */,
                                A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
-                               A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
+                               A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
                                A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */,
-                               A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
+                               A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
                                A7E9B67312D37EC400DA6239 /* catchallcommand.h */,
-                               A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */,
+                               A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
                                A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */,
-                               A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */,
+                               A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */,
                                A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */,
-                               A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */,
+                               A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */,
                                A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */,
-                               A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */,
+                               A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */,
                                A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */,
-                               A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */,
-                               A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */,
-                               A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */,
+                               A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */,
                                A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */,
-                               A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */,
+                               A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */,
                                A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */,
-                               A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */,
+                               A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */,
                                A7E9B69112D37EC400DA6239 /* classifyotucommand.h */,
-                               A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
+                               A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */,
                                A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */,
-                               A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */,
+                               A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
                                A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
-                               A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */,
+                               A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */,
                                A7E9B69D12D37EC400DA6239 /* clustercommand.h */,
-                               A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */,
+                               A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */,
                                A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */,
-                               A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */,
+                               A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */,
                                A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */,
-                               A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */,
+                               A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */,
                                A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */,
-                               A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */,
+                               A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */,
                                A7E9B6A912D37EC400DA6239 /* collectcommand.h */,
-                               A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */,
+                               A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */,
                                A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */,
-                               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */,
+                               A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */,
                                A7E9B6B612D37EC400DA6239 /* consensuscommand.h */,
-                               A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
+                               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */,
                                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */,
-                               A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+                               A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
                                A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
-                               A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
+                               A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
                                A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
-                               A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */,
+                               A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
                                A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */,
-                               A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */,
+                               A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */,
                                A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */,
-                               A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
+                               A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */,
                                A7E9B6CC12D37EC400DA6239 /* distancecommand.h */,
-                               A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
+                               A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
                                A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
-                               A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
+                               A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
+                               A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */,
+                               A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */,
+                               A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
+                               A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
                                A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
-                               A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
+                               A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
                                A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */,
-                               A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
+                               A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
                                A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */,
-                               A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
+                               A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
                                A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */,
-                               A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */,
+                               A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
                                A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */,
-                               A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */,
+                               A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */,
                                A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */,
-                               A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */,
+                               A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */,
                                A7E9B70112D37EC400DA6239 /* getotuscommand.h */,
-                               A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */,
+                               A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */,
                                A7E9B70312D37EC400DA6239 /* getrabundcommand.h */,
-                               A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */,
+                               A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */,
                                A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */,
-                               A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */,
+                               A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */,
                                A7E9B70712D37EC400DA6239 /* getsabundcommand.h */,
-                               A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */,
+                               A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */,
                                A7E9B70912D37EC400DA6239 /* getseqscommand.h */,
-                               A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */,
+                               A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */,
                                A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */,
-                               A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */,
+                               A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */,
                                A7E9B71B12D37EC400DA6239 /* hclustercommand.h */,
-                               A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */,
+                               A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */,
                                A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */,
-                               A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */,
+                               A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */,
                                A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */,
-                               A7E9B72812D37EC400DA6239 /* helpcommand.cpp */,
+                               A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */,
                                A7E9B72912D37EC400DA6239 /* helpcommand.h */,
-                               A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
+                               A7E9B72812D37EC400DA6239 /* helpcommand.cpp */,
+                               A75790571301749D00A30DAB /* homovacommand.h */,
+                               A75790581301749D00A30DAB /* homovacommand.cpp */,
                                A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */,
-                               A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
+                               A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
                                A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
-                               A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
+                               A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
                                A7E9B73E12D37EC400DA6239 /* listseqscommand.h */,
-                               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */,
+                               A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
+                               A7FA10001302E096003860FE /* mantelcommand.h */,
+                               A7FA10011302E096003860FE /* mantelcommand.cpp */,
+                               A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */,
+                               A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */,
                                A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
-                               A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
+                               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */,
                                A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
-                               A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
+                               A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
                                A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
+                               A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
                                A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
                                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
-                               A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
                                A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
-                               A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
+                               A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
                                A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */,
+                               A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
                                A7E9B76A12D37EC400DA6239 /* nocommands.h */,
                                A7E9B76912D37EC400DA6239 /* nocommands.cpp */,
-                               A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
                                A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */,
+                               A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
                                A713EBEB12DC7C5E000092AC /* nmdscommand.h */,
                                A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */,
-                               A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */,
                                A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */,
-                               A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */,
+                               A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */,
                                A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */,
-                               A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */,
+                               A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */,
                                A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */,
-                               A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */,
+                               A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */,
                                A7E9B78212D37EC400DA6239 /* parselistscommand.h */,
-                               A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
+                               A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */,
                                A7E9B78612D37EC400DA6239 /* parsimonycommand.h */,
+                               A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
                                A7FC486512D795D60055BC5C /* pcacommand.h */,
                                A7FC486612D795D60055BC5C /* pcacommand.cpp */,
-                               A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
                                A7E9B78812D37EC400DA6239 /* pcoacommand.h */,
-                               A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
+                               A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
                                A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */,
-                               A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */,
+                               A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
                                A7E9B79212D37EC400DA6239 /* phylotypecommand.h */,
-                               A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */,
+                               A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */,
                                A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */,
-                               A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */,
+                               A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */,
                                A7E9B79812D37EC400DA6239 /* preclustercommand.h */,
-                               A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */,
+                               A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */,
                                A7E9B7A212D37EC400DA6239 /* quitcommand.h */,
-                               A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
+                               A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */,
                                A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */,
-                               A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
+                               A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
                                A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
-                               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */,
+                               A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
                                A7E9B7B712D37EC400DA6239 /* readdistcommand.h */,
-                               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */,
+                               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */,
                                A7E9B7BC12D37EC400DA6239 /* readotucommand.h */,
-                               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */,
+                               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */,
                                A7E9B7C212D37EC400DA6239 /* readtreecommand.h */,
-                               A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
+                               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */,
                                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
-                               A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */,
+                               A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
                                A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
-                               A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
+                               A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */,
                                A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
+                               A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
                                A727864212E9E28C00F86ABA /* removerarecommand.h */,
                                A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
-                               A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
                                A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
-                               A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
+                               A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
                                A7E9B7CE12D37EC400DA6239 /* reversecommand.h */,
-                               A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */,
+                               A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
                                A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */,
-                               A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */,
+                               A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */,
                                A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */,
-                               A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */,
+                               A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */,
                                A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */,
-                               A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */,
+                               A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */,
                                A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */,
-                               A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */,
+                               A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */,
                                A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */,
-                               A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */,
+                               A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */,
+                               A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */,
+                               A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */,
                                A7E9B7E012D37EC400DA6239 /* setdircommand.h */,
-                               A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
+                               A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */,
                                A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */,
-                               A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
+                               A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
                                A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */,
-                               A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
+                               A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
                                A7E9B7F312D37EC400DA6239 /* sharedcommand.h */,
-                               A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */,
+                               A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
-                               A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
+                               A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */,
                                A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
-                               A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */,
+                               A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
                                A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
-                               A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */,
+                               A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */,
                                A7E9B85012D37EC400DA6239 /* subsamplecommand.h */,
-                               A7E9B85712D37EC400DA6239 /* summarycommand.cpp */,
+                               A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */,
                                A7E9B85812D37EC400DA6239 /* summarycommand.h */,
-                               A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
+                               A7E9B85712D37EC400DA6239 /* summarycommand.cpp */,
                                A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */,
-                               A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */,
+                               A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
                                A7E9B85C12D37EC400DA6239 /* systemcommand.h */,
-                               A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */,
+                               A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */,
                                A7E9B86312D37EC400DA6239 /* treegroupscommand.h */,
-                               A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */,
+                               A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */,
                                A7E9B86912D37EC400DA6239 /* trimflowscommand.h */,
-                               A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */,
+                               A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */,
                                A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */,
-                               A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */,
+                               A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */,
                                A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */,
-                               A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */,
+                               A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */,
                                A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */,
-                               A7E9B87A12D37EC400DA6239 /* venncommand.cpp */,
+                               A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */,
                                A7E9B87B12D37EC400DA6239 /* venncommand.h */,
+                               A7E9B87A12D37EC400DA6239 /* venncommand.cpp */,
                        );
                        name = commands;
                        sourceTree = "<group>";
                                A7E9B84D12D37EC400DA6239 /* structpearson.cpp */,
                                A7E9B84E12D37EC400DA6239 /* structpearson.h */,
                                A7E9B86112D37EC400DA6239 /* treecalculator.h */,
-                               A7E9B87012D37EC400DA6239 /* unweighted.cpp */,
                                A7E9B87112D37EC400DA6239 /* unweighted.h */,
+                               A7E9B87012D37EC400DA6239 /* unweighted.cpp */,
                                A7E9B87212D37EC400DA6239 /* uvest.cpp */,
                                A7E9B87312D37EC400DA6239 /* uvest.h */,
-                               A7E9B87C12D37EC400DA6239 /* weighted.cpp */,
                                A7E9B87D12D37EC400DA6239 /* weighted.h */,
+                               A7E9B87C12D37EC400DA6239 /* weighted.cpp */,
                                A7E9B87F12D37EC400DA6239 /* whittaker.cpp */,
                                A7E9B88012D37EC400DA6239 /* whittaker.h */,
                        );
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
                                A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */,
                                A7E9B80512D37EC400DA6239 /* sharedlistvector.h */,
-                               A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
                                A7E9B80E12D37EC400DA6239 /* sharedordervector.h */,
+                               A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
                                A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
                                A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */,
                                A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */,
                                A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */,
                                A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
                                A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
-                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
                                A7E9B74612D37EC400DA6239 /* maligner.h */,
+                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
                                A7E9B74512D37EC400DA6239 /* maligner.cpp */,
                                A7E9B79312D37EC400DA6239 /* pintail.cpp */,
                                A7E9B79412D37EC400DA6239 /* pintail.h */,
                                A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */,
                                A7E9B7B512D37EC400DA6239 /* readcolumn.h */,
                                A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */,
-                               A7E9B7B912D37EC400DA6239 /* readotu.cpp */,
-                               A7E9B7BA12D37EC400DA6239 /* readotu.h */,
                                A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */,
                                A7E9B7BE12D37EC400DA6239 /* readphylip.h */,
                                A7E9B7BF12D37EC400DA6239 /* readtree.cpp */,
                        attributes = {
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
-                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
+                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
                        compatibilityVersion = "Xcode 3.1";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
                                A7E9B89A12D37EC400DA6239 /* chimeracheckrdp.cpp in Sources */,
                                A7E9B89B12D37EC400DA6239 /* chimerapintailcommand.cpp in Sources */,
                                A7E9B89C12D37EC400DA6239 /* chimerarealigner.cpp in Sources */,
-                               A7E9B89D12D37EC400DA6239 /* chimeraseqscommand.cpp in Sources */,
                                A7E9B89E12D37EC400DA6239 /* chimeraslayer.cpp in Sources */,
                                A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */,
                                A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */,
                                A7E9B8D712D37EC400DA6239 /* getsabundcommand.cpp in Sources */,
                                A7E9B8D812D37EC400DA6239 /* getseqscommand.cpp in Sources */,
                                A7E9B8D912D37EC400DA6239 /* getsharedotucommand.cpp in Sources */,
-                               A7E9B8DA12D37EC400DA6239 /* globaldata.cpp in Sources */,
                                A7E9B8DB12D37EC400DA6239 /* goodscoverage.cpp in Sources */,
                                A7E9B8DC12D37EC400DA6239 /* gotohoverlap.cpp in Sources */,
                                A7E9B8DD12D37EC400DA6239 /* gower.cpp in Sources */,
                                A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */,
                                A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */,
                                A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */,
-                               A7E9B92D12D37EC400DA6239 /* readotu.cpp in Sources */,
                                A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */,
                                A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */,
                                A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */,
                                A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */,
                                A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */,
                                A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */,
+                               7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */,
+                               A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */,
+                               A75790591301749D00A30DAB /* homovacommand.cpp in Sources */,
+                               A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */,
+                               A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */,
+                               A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */,
+                               A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */,
+                               A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */,
+                               A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                GCC_OPTIMIZATION_LEVEL = 0;
                                INSTALL_PATH = /usr/local/bin;
                                PRODUCT_NAME = Mothur;
+                               SDKROOT = macosx10.6;
                        };
                        name = Debug;
                };
                1DEB928A08733DD80010E9CD /* Debug */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
+                               ARCHS = "$(ARCHS_STANDARD_64_BIT)";
                                DEPLOYMENT_LOCATION = NO;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
-                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.16.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"1/26/2010\\\"\"",
+                                       "VERSION=\"\\\"1.18.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"4/11/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                INSTALL_PATH = "";
+                               MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                OTHER_CPLUSPLUSFLAGS = (
-                                       "-DUSE_READLINE",
                                        "-DBIT_VERSION",
+                                       "-DUSE_READLINE",
                                        "$(OTHER_CFLAGS)",
                                );
                                OTHER_LDFLAGS = (
                                        "-lreadline",
                                );
                                PREBINDING = NO;
-                               SDKROOT = macosx10.5;
+                               SDKROOT = macosx10.6;
                        };
                        name = Debug;
                };
                1DEB928B08733DD80010E9CD /* Release */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
+                               ARCHS = "$(ARCHS_STANDARD_64_BIT)";
                                DEPLOYMENT_LOCATION = NO;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
+                               GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
+                               GCC_MODEL_TUNING = "";
+                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.15.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
+                                       "VERSION=\"\\\"1.18.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"4/11/2011\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                INSTALL_PATH = "";
+                               MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-DUSE_READLINE",
                                        "-DBIT_VERSION",
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
                                1DEB928A08733DD80010E9CD /* Debug */,