archiveVersion = 1;
classes = {
};
- objectVersion = 45;
+ objectVersion = 46;
objects = {
/* Begin PBXBuildFile section */
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 */; };
+ A721765713BB9F7D0014DAAE /* referencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721765613BB9F7D0014DAAE /* referencedb.cpp */; };
+ A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A724D2B6153C8628000A826F /* makebiomcommand.cpp */; };
A727864412E9E28C00F86ABA /* removerarecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A727864312E9E28C00F86ABA /* removerarecommand.cpp */; };
+ A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; };
+ A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */; };
+ A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74A9A9E148E881E00AB5E3E /* spline.cpp */; };
+ A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */; };
+ A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A754149614840CF7005850D1 /* summaryqualcommand.cpp */; };
A75790591301749D00A30DAB /* homovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A75790581301749D00A30DAB /* homovacommand.cpp */; };
+ A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A76CDD811510F143004C8458 /* prcseqscommand.cpp */; };
+ A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7730EFE13967241007433A3 /* countseqscommand.cpp */; };
+ A774101414695AF60098E6AC /* shhhseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A774101314695AF60098E6AC /* shhhseqscommand.cpp */; };
+ A774104814696F320098E6AC /* myseqdist.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A774104614696F320098E6AC /* myseqdist.cpp */; };
+ A77410F614697C300098E6AC /* seqnoise.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77410F414697C300098E6AC /* seqnoise.cpp */; };
+ A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */; };
+ A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */; };
+ A77EBD2F1523709100ED407C /* createdatabasecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A77EBD2E1523709100ED407C /* createdatabasecommand.cpp */; };
+ A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7876A25152A017C00A0AE86 /* subsample.cpp */; };
+ A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A79234D613C74BF6002B08E2 /* mothurfisher.cpp */; };
+ A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A795840C13F13CD900F201D5 /* countgroupscommand.cpp */; };
A799F5B91309A3E000AEEFA0 /* makefastqcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */; };
+ A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */; };
+ A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */; };
A7A61F2D130062E000E05B6B /* amovacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A61F2C130062E000E05B6B /* amovacommand.cpp */; };
+ A7BF221414587886000AD524 /* myPerseus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7BF221214587886000AD524 /* myPerseus.cpp */; };
+ A7BF2232145879B2000AD524 /* chimeraperseuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */; };
+ A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */; };
+ A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */; };
+ A7D755DA1535F679009BF21A /* treereader.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7D755D91535F679009BF21A /* treereader.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 */; };
A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66412D37EC400DA6239 /* blastdb.cpp */; };
A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66612D37EC400DA6239 /* boneh.cpp */; };
A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66812D37EC400DA6239 /* bootstrap.cpp */; };
- A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */; };
A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66C12D37EC400DA6239 /* bstick.cpp */; };
A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B66E12D37EC400DA6239 /* calculator.cpp */; };
A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B67012D37EC400DA6239 /* canberra.cpp */; };
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 */; };
A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */; };
A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */; };
A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */; };
- A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */; };
+ A7E9B8B312D37EC400DA6239 /* consensus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B512D37EC400DA6239 /* consensus.cpp */; };
A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */; };
A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */; };
A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6BB12D37EC400DA6239 /* coverage.cpp */; };
A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */; };
A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */; };
A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */; };
- A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E512D37EC400DA6239 /* fisher2.c */; };
A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E712D37EC400DA6239 /* flowdata.cpp */; };
A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */; };
A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B6EC12D37EC400DA6239 /* formatphylip.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 */; };
A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */; };
A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75112D37EC400DA6239 /* mempearson.cpp */; };
A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */; };
- A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75612D37EC400DA6239 /* metastats2.c */; };
A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */; };
A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */; };
A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B75B12D37EC400DA6239 /* mothur.cpp */; };
A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78312D37EC400DA6239 /* parsimony.cpp */; };
A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */; };
A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */; };
- A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */; };
A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */; };
A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */; };
A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B78F12D37EC400DA6239 /* phylotree.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 */; };
+ A7EEB0F514F29BFE00344B83 /* classifytreecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */; };
+ A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */; };
A7FA10021302E097003860FE /* mantelcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FA10011302E096003860FE /* mantelcommand.cpp */; };
+ A7FA2AC714A0E881007C09A6 /* bsplvb.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2ABC14A0E881007C09A6 /* bsplvb.f */; };
+ A7FA2AC814A0E881007C09A6 /* bsplvd.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2ABD14A0E881007C09A6 /* bsplvd.f */; };
+ A7FA2AC914A0E881007C09A6 /* bvalue.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2ABE14A0E881007C09A6 /* bvalue.f */; };
+ A7FA2ACA14A0E881007C09A6 /* daxpy.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2ABF14A0E881007C09A6 /* daxpy.f */; };
+ A7FA2ACB14A0E881007C09A6 /* ddot.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC014A0E881007C09A6 /* ddot.f */; };
+ A7FA2ACC14A0E881007C09A6 /* dpbfa.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC114A0E881007C09A6 /* dpbfa.f */; };
+ A7FA2ACD14A0E881007C09A6 /* dpbsl.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC214A0E881007C09A6 /* dpbsl.f */; };
+ A7FA2ACE14A0E881007C09A6 /* interv.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC314A0E881007C09A6 /* interv.f */; };
+ A7FA2ACF14A0E881007C09A6 /* sgram.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC414A0E881007C09A6 /* sgram.f */; };
+ A7FA2AD014A0E881007C09A6 /* sinerp.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC514A0E881007C09A6 /* sinerp.f */; };
+ A7FA2AD114A0E881007C09A6 /* stxwx.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC614A0E881007C09A6 /* stxwx.f */; };
+ A7FA2B1614A0EBEA007C09A6 /* sslvrg.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2B1514A0EBEA007C09A6 /* sslvrg.f */; };
+ A7FA2B5B14A0F0C2007C09A6 /* intrv.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2B5A14A0F0C2007C09A6 /* intrv.f */; };
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 */; };
+ A7FF19F2140FFDA500AD216D /* trimoligos.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FF19F1140FFDA500AD216D /* trimoligos.cpp */; };
+ A7FFB558142CA02C004884F2 /* summarytaxcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */; };
/* End PBXBuildFile section */
+/* Begin PBXBuildRule section */
+ A7D162CB149F96CA000523E8 /* PBXBuildRule */ = {
+ isa = PBXBuildRule;
+ compilerSpec = com.apple.compilers.proxy.script;
+ fileType = sourcecode.fortran;
+ isEditable = 1;
+ outputFiles = (
+ "$(TARGET_BUILD_DIR)/$(INPUT_FILE_BASE).o",
+ );
+ script = "/usr/local/gfortran/bin/gfortran -g -m64 -c ${PROJECT_DIR}/${INPUT_FILE_NAME} -o ${TARGET_BUILD_DIR}/${INPUT_FILE_BASE}.o";
+ };
+/* End PBXBuildRule section */
+
/* Begin PBXCopyFilesBuildPhase section */
8DD76FAF0486AB0100D96B5E /* CopyFiles */ = {
isa = PBXCopyFilesBuildPhase;
/* 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>"; };
+ 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; 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>"; };
+ A721765513BB9F7D0014DAAE /* referencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = referencedb.h; sourceTree = "<group>"; };
+ A721765613BB9F7D0014DAAE /* referencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = referencedb.cpp; sourceTree = "<group>"; };
+ A724D2B4153C8600000A826F /* makebiomcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makebiomcommand.h; sourceTree = "<group>"; };
+ A724D2B6153C8628000A826F /* makebiomcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makebiomcommand.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>"; };
+ A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearmemorycommand.h; sourceTree = "<group>"; };
+ A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearmemorycommand.cpp; sourceTree = "<group>"; };
+ A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurmetastats.h; sourceTree = "<group>"; };
+ A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurmetastats.cpp; sourceTree = "<group>"; };
+ A74A9A9D148E881E00AB5E3E /* spline.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spline.h; sourceTree = "<group>"; };
+ A74A9A9E148E881E00AB5E3E /* spline.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = spline.cpp; sourceTree = "<group>"; };
+ A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerauchimecommand.h; sourceTree = "<group>"; };
+ A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerauchimecommand.cpp; sourceTree = "<group>"; };
+ A754149514840CF7005850D1 /* summaryqualcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summaryqualcommand.h; sourceTree = "<group>"; };
+ A754149614840CF7005850D1 /* summaryqualcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summaryqualcommand.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>"; };
+ A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcrseqscommand.h; sourceTree = "<group>"; };
+ A76CDD811510F143004C8458 /* prcseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = prcseqscommand.cpp; sourceTree = "<group>"; };
+ A7730EFD13967241007433A3 /* countseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = countseqscommand.h; sourceTree = "<group>"; };
+ A7730EFE13967241007433A3 /* countseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countseqscommand.cpp; sourceTree = "<group>"; };
+ A774101214695AF60098E6AC /* shhhseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shhhseqscommand.h; sourceTree = "<group>"; };
+ A774101314695AF60098E6AC /* shhhseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shhhseqscommand.cpp; sourceTree = "<group>"; };
+ A774104614696F320098E6AC /* myseqdist.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = myseqdist.cpp; sourceTree = "<group>"; };
+ A774104714696F320098E6AC /* myseqdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myseqdist.h; sourceTree = "<group>"; };
+ A77410F414697C300098E6AC /* seqnoise.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqnoise.cpp; sourceTree = "<group>"; };
+ A77410F514697C300098E6AC /* seqnoise.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqnoise.h; 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>"; };
+ A77A221D139001B600B0BE70 /* deuniquetreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deuniquetreecommand.h; sourceTree = "<group>"; };
+ A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deuniquetreecommand.cpp; sourceTree = "<group>"; };
+ A77EBD2C1523707F00ED407C /* createdatabasecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = createdatabasecommand.h; sourceTree = "<group>"; };
+ A77EBD2E1523709100ED407C /* createdatabasecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = createdatabasecommand.cpp; sourceTree = "<group>"; };
+ A7876A25152A017C00A0AE86 /* subsample.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsample.cpp; sourceTree = "<group>"; };
+ A7876A28152A018B00A0AE86 /* subsample.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsample.h; sourceTree = "<group>"; };
+ A79234D513C74BF6002B08E2 /* mothurfisher.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurfisher.h; sourceTree = "<group>"; };
+ A79234D613C74BF6002B08E2 /* mothurfisher.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurfisher.cpp; sourceTree = "<group>"; };
+ A795840B13F13CD900F201D5 /* countgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = countgroupscommand.h; sourceTree = "<group>"; };
+ A795840C13F13CD900F201D5 /* countgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countgroupscommand.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>"; };
+ A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sortseqscommand.cpp; sourceTree = "<group>"; };
+ A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sortseqscommand.h; sourceTree = "<group>"; };
+ A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuassociationcommand.cpp; sourceTree = "<group>"; };
+ A7A3C8C814D041AD00B1BFBE /* otuassociationcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuassociationcommand.h; 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>"; };
+ A7BF221214587886000AD524 /* myPerseus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = myPerseus.cpp; sourceTree = "<group>"; };
+ A7BF221314587886000AD524 /* myPerseus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myPerseus.h; sourceTree = "<group>"; };
+ A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraperseuscommand.h; sourceTree = "<group>"; };
+ A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraperseuscommand.cpp; sourceTree = "<group>"; };
+ A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cooccurrencecommand.cpp; sourceTree = "<group>"; };
+ A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cooccurrencecommand.h; sourceTree = "<group>"; };
+ A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trialSwap2.cpp; sourceTree = "<group>"; };
+ A7C3DC0E14FE469500FE1924 /* trialswap2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trialswap2.h; sourceTree = "<group>"; };
+ A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = "<group>"; };
+ A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treereader.cpp; 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>"; };
A7E9B66712D37EC400DA6239 /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = "<group>"; };
A7E9B66812D37EC400DA6239 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = "<group>"; };
A7E9B66912D37EC400DA6239 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = "<group>"; };
- A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrapsharedcommand.cpp; sourceTree = "<group>"; };
- A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrapsharedcommand.h; sourceTree = "<group>"; };
A7E9B66C12D37EC400DA6239 /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = "<group>"; };
A7E9B66D12D37EC400DA6239 /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = "<group>"; };
A7E9B66E12D37EC400DA6239 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.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>"; };
A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = SOURCE_ROOT; };
A7E9B6B312D37EC400DA6239 /* common.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = common.h; sourceTree = "<group>"; };
A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; };
- A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = "<group>"; };
- A7E9B6B612D37EC400DA6239 /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = "<group>"; };
+ A7E9B6B512D37EC400DA6239 /* consensus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensus.cpp; sourceTree = "<group>"; };
+ A7E9B6B612D37EC400DA6239 /* consensus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensus.h; sourceTree = "<group>"; };
A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensusseqscommand.cpp; sourceTree = "<group>"; };
A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensusseqscommand.h; sourceTree = "<group>"; };
A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = corraxescommand.cpp; sourceTree = "<group>"; };
A7E9B6E212D37EC400DA6239 /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = "<group>"; };
A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = "<group>"; };
A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = "<group>"; };
- A7E9B6E512D37EC400DA6239 /* fisher2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = fisher2.c; sourceTree = "<group>"; };
- A7E9B6E612D37EC400DA6239 /* fisher2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fisher2.h; sourceTree = "<group>"; };
A7E9B6E712D37EC400DA6239 /* flowdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = flowdata.cpp; sourceTree = "<group>"; };
A7E9B6E812D37EC400DA6239 /* flowdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = flowdata.h; sourceTree = "<group>"; };
A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.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; };
A7E9B75212D37EC400DA6239 /* mempearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mempearson.h; sourceTree = "<group>"; };
A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = "<group>"; };
A7E9B75412D37EC400DA6239 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = "<group>"; };
- A7E9B75512D37EC400DA6239 /* metastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastats.h; sourceTree = "<group>"; };
- A7E9B75612D37EC400DA6239 /* metastats2.c */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.c; path = metastats2.c; sourceTree = "<group>"; };
A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = "<group>"; };
A7E9B75812D37EC400DA6239 /* metastatscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastatscommand.h; sourceTree = "<group>"; };
A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = "<group>"; };
A7E9B78612D37EC400DA6239 /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = "<group>"; };
A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = "<group>"; };
- A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
- A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = "<group>"; };
A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
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>"; };
- A7E9B7BA12D37EC400DA6239 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = "<group>"; };
A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
A7E9B7E812D37EC400DA6239 /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = "<group>"; };
A7E9B7E912D37EC400DA6239 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
A7E9B7EA12D37EC400DA6239 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
- A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = "<group>"; };
A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = "<group>"; };
A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = "<group>"; };
A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
A7E9B84E12D37EC400DA6239 /* structpearson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structpearson.h; sourceTree = "<group>"; };
A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = "<group>"; };
A7E9B85012D37EC400DA6239 /* subsamplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsamplecommand.h; sourceTree = "<group>"; };
- A7E9B85112D37EC400DA6239 /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = SOURCE_ROOT; };
- A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = SOURCE_ROOT; };
- A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = SOURCE_ROOT; };
- A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = SOURCE_ROOT; };
- A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = SOURCE_ROOT; };
- A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = SOURCE_ROOT; };
+ A7E9B85112D37EC400DA6239 /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = "<group>"; };
+ A7E9B85212D37EC400DA6239 /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = "<group>"; };
+ A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = "<group>"; };
+ A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = "<group>"; };
+ A7E9B85512D37EC400DA6239 /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = "<group>"; };
+ A7E9B85612D37EC400DA6239 /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = "<group>"; };
A7E9B85712D37EC400DA6239 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = "<group>"; };
A7E9B85812D37EC400DA6239 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = "<group>"; };
A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; };
A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
A7E9B88012D37EC400DA6239 /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
+ A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifytreecommand.cpp; sourceTree = "<group>"; };
+ A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifytreecommand.h; sourceTree = "<group>"; };
+ A7F9F5CD141A5E500032F693 /* sequenceparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequenceparser.h; sourceTree = "<group>"; };
+ A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequenceparser.cpp; sourceTree = "<group>"; };
A7FA10001302E096003860FE /* mantelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mantelcommand.h; sourceTree = "<group>"; };
A7FA10011302E096003860FE /* mantelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mantelcommand.cpp; sourceTree = "<group>"; };
+ A7FA2ABC14A0E881007C09A6 /* bsplvb.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = bsplvb.f; sourceTree = "<group>"; };
+ A7FA2ABD14A0E881007C09A6 /* bsplvd.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = bsplvd.f; sourceTree = "<group>"; };
+ A7FA2ABE14A0E881007C09A6 /* bvalue.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = bvalue.f; sourceTree = "<group>"; };
+ A7FA2ABF14A0E881007C09A6 /* daxpy.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = daxpy.f; sourceTree = "<group>"; };
+ A7FA2AC014A0E881007C09A6 /* ddot.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = ddot.f; sourceTree = "<group>"; };
+ A7FA2AC114A0E881007C09A6 /* dpbfa.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = dpbfa.f; sourceTree = "<group>"; };
+ A7FA2AC214A0E881007C09A6 /* dpbsl.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = dpbsl.f; sourceTree = "<group>"; };
+ A7FA2AC314A0E881007C09A6 /* interv.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = interv.f; sourceTree = "<group>"; };
+ A7FA2AC414A0E881007C09A6 /* sgram.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = sgram.f; sourceTree = "<group>"; };
+ A7FA2AC514A0E881007C09A6 /* sinerp.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = sinerp.f; sourceTree = "<group>"; };
+ A7FA2AC614A0E881007C09A6 /* stxwx.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = stxwx.f; sourceTree = "<group>"; };
+ A7FA2B1514A0EBEA007C09A6 /* sslvrg.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = sslvrg.f; sourceTree = "<group>"; };
+ A7FA2B5A14A0F0C2007C09A6 /* intrv.f */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.fortran; path = intrv.f; sourceTree = "<group>"; };
A7FC480C12D788F20055BC5C /* linearalgebra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = linearalgebra.h; sourceTree = "<group>"; };
A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = "<group>"; };
A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = "<group>"; };
A7FC486612D795D60055BC5C /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = "<group>"; };
+ A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcurrentcommand.h; sourceTree = "<group>"; };
+ 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>"; };
+ A7FF19F0140FFDA500AD216D /* trimoligos.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimoligos.h; sourceTree = "<group>"; };
+ A7FF19F1140FFDA500AD216D /* trimoligos.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimoligos.cpp; sourceTree = "<group>"; };
+ A7FFB556142CA02C004884F2 /* summarytaxcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarytaxcommand.h; sourceTree = "<group>"; };
+ A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarytaxcommand.cpp; sourceTree = "<group>"; };
C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = "<group>"; };
/* End PBXFileReference section */
A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */,
A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */,
A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */,
+ A7DAAFA3133A254E003956EB /* commandparameter.h */,
A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
A7E9BA4212D3960D00DA6239 /* containers */,
+ A7E9B6B612D37EC400DA6239 /* consensus.h */,
+ A7E9B6B512D37EC400DA6239 /* consensus.cpp */,
+ 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 */,
+ A774104714696F320098E6AC /* myseqdist.h */,
+ A774104614696F320098E6AC /* myseqdist.cpp */,
A7E9B76112D37EC400DA6239 /* nast.cpp */,
A7E9B76212D37EC400DA6239 /* nast.hpp */,
A7E9B76312D37EC400DA6239 /* nastreport.cpp */,
A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */,
7E6BE10812F710D8007ADDBE /* refchimeratest.h */,
7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */,
+ A77410F514697C300098E6AC /* seqnoise.h */,
+ A77410F414697C300098E6AC /* seqnoise.cpp */,
A7E9BA5312D39A5E00DA6239 /* read */,
A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */,
A7E9B82412D37EC400DA6239 /* sharedutilities.h */,
A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
A7E9B83112D37EC400DA6239 /* slibshuff.h */,
- A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
- A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
- A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
- A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
- A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
- A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
+ A7876A28152A018B00A0AE86 /* subsample.h */,
+ A7876A25152A017C00A0AE86 /* subsample.cpp */,
+ A7C3DC0E14FE469500FE1924 /* trialswap2.h */,
+ A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */,
+ A7FF19F0140FFDA500AD216D /* trimoligos.h */,
+ A7FF19F1140FFDA500AD216D /* trimoligos.cpp */,
A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
A7E9B87512D37EC400DA6239 /* validcalculator.h */,
A7E9B87612D37EC400DA6239 /* validparameter.cpp */,
name = Products;
sourceTree = "<group>";
};
+ A7D161E7149F7F50000523E8 /* fortran */ = {
+ isa = PBXGroup;
+ children = (
+ A7FA2B5A14A0F0C2007C09A6 /* intrv.f */,
+ A7FA2B1514A0EBEA007C09A6 /* sslvrg.f */,
+ A7FA2ABC14A0E881007C09A6 /* bsplvb.f */,
+ A7FA2ABD14A0E881007C09A6 /* bsplvd.f */,
+ A7FA2ABE14A0E881007C09A6 /* bvalue.f */,
+ A7FA2ABF14A0E881007C09A6 /* daxpy.f */,
+ A7FA2AC014A0E881007C09A6 /* ddot.f */,
+ A7FA2AC114A0E881007C09A6 /* dpbfa.f */,
+ A7FA2AC214A0E881007C09A6 /* dpbsl.f */,
+ A7FA2AC314A0E881007C09A6 /* interv.f */,
+ A7FA2AC414A0E881007C09A6 /* sgram.f */,
+ A7FA2AC514A0E881007C09A6 /* sinerp.f */,
+ A7FA2AC614A0E881007C09A6 /* stxwx.f */,
+ );
+ name = fortran;
+ sourceTree = "<group>";
+ };
A7E9BA3812D3956100DA6239 /* commands */ = {
isa = PBXGroup;
children = (
A7E9B6AE12D37EC400DA6239 /* command.hpp */,
- A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
A7E9B65212D37EC300DA6239 /* aligncommand.h */,
+ A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
A7A61F2B130062E000E05B6B /* amovacommand.h */,
A7A61F2C130062E000E05B6B /* amovacommand.cpp */,
- A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
+ A71CB15F130B04A2001E7287 /* anosimcommand.h */,
+ A71CB15E130B04A2001E7287 /* anosimcommand.cpp */,
A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
- A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
- A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */,
- A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
+ A7E9B66012D37EC300DA6239 /* binsequencecommand.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 */,
+ A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */,
+ A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */,
A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */,
- A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */,
+ A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */,
+ A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */,
+ A74D36B7137DAFAA00332B0C /* chimerauchimecommand.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 */,
+ A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */,
+ A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */,
A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
- A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */,
+ A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */,
+ A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */,
+ A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.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 */,
- A7E9B6B612D37EC400DA6239 /* consensuscommand.h */,
- A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
+ A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */,
A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */,
- A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+ A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
+ A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */,
+ A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */,
A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
- A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
+ A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+ A795840B13F13CD900F201D5 /* countgroupscommand.h */,
+ A795840C13F13CD900F201D5 /* countgroupscommand.cpp */,
+ A7730EFD13967241007433A3 /* countseqscommand.h */,
+ A7730EFE13967241007433A3 /* countseqscommand.cpp */,
+ A77EBD2C1523707F00ED407C /* createdatabasecommand.h */,
+ A77EBD2E1523709100ED407C /* createdatabasecommand.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 */,
+ A77A221D139001B600B0BE70 /* deuniquetreecommand.h */,
+ A77A221E139001B600B0BE70 /* deuniquetreecommand.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 */,
+ A7E9B72812D37EC400DA6239 /* helpcommand.cpp */,
A75790571301749D00A30DAB /* homovacommand.h */,
A75790581301749D00A30DAB /* homovacommand.cpp */,
- A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */,
- A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
+ A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
- A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
+ A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
A7E9B73E12D37EC400DA6239 /* listseqscommand.h */,
+ A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
A7FA10001302E096003860FE /* mantelcommand.h */,
A7FA10011302E096003860FE /* mantelcommand.cpp */,
+ A724D2B4153C8600000A826F /* makebiomcommand.h */,
+ A724D2B6153C8628000A826F /* makebiomcommand.cpp */,
A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */,
A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */,
- A7E9B74312D37EC400DA6239 /* makegroupcommand.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 */,
+ A7A3C8C814D041AD00B1BFBE /* otuassociationcommand.h */,
+ A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.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 */,
+ A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */,
+ A76CDD811510F143004C8458 /* prcseqscommand.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 */,
+ A774101214695AF60098E6AC /* shhhseqscommand.h */,
+ A774101314695AF60098E6AC /* shhhseqscommand.cpp */,
+ A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */,
+ A7A32DA914DC43B00001D2E5 /* sortseqscommand.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 */,
+ A754149514840CF7005850D1 /* summaryqualcommand.h */,
+ A754149614840CF7005850D1 /* summaryqualcommand.cpp */,
A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */,
- A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */,
+ A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
+ A7FFB556142CA02C004884F2 /* summarytaxcommand.h */,
+ A7FFB557142CA02C004884F2 /* summarytaxcommand.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>";
A7E9BA3F12D395F700DA6239 /* calculators */ = {
isa = PBXGroup;
children = (
+ 7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */,
A7E9B64F12D37EC300DA6239 /* ace.cpp */,
A7E9B65012D37EC300DA6239 /* ace.h */,
A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */,
A7E9B6D712D37EC400DA6239 /* efron.cpp */,
A7E9B6D812D37EC400DA6239 /* efron.h */,
A7E9B6E212D37EC400DA6239 /* filters.h */,
- A7E9B6E512D37EC400DA6239 /* fisher2.c */,
- A7E9B6E612D37EC400DA6239 /* fisher2.h */,
A7E9B6F012D37EC400DA6239 /* geom.cpp */,
A7E9B6F112D37EC400DA6239 /* geom.h */,
A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */,
A7E9B7E812D37EC400DA6239 /* shannoneven.h */,
A7E9B7E912D37EC400DA6239 /* sharedace.cpp */,
A7E9B7EA12D37EC400DA6239 /* sharedace.h */,
- A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */,
A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */,
A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */,
A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */,
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 */,
);
A7E9B7A012D37EC400DA6239 /* qualityscores.h */,
A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */,
A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */,
+ A721765513BB9F7D0014DAAE /* referencedb.h */,
+ A721765613BB9F7D0014DAAE /* referencedb.cpp */,
A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */,
A7E9B7CC12D37EC400DA6239 /* reportfile.h */,
A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */,
A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
+ A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
+ A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */,
A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */,
A7E9B80512D37EC400DA6239 /* sharedlistvector.h */,
- A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
A7E9B80E12D37EC400DA6239 /* sharedordervector.h */,
- A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
+ A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */,
+ A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */,
A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */,
A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */,
A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+ A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
+ A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
+ A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
+ A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
+ A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
+ A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
A7E9B85F12D37EC400DA6239 /* tree.cpp */,
A7E9B86012D37EC400DA6239 /* tree.h */,
A7E9B86412D37EC400DA6239 /* treemap.cpp */,
A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */,
A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */,
A7E9B68512D37EC400DA6239 /* chimerarealigner.h */,
+ A7E9B6C212D37EC400DA6239 /* decalc.h */,
+ A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */,
A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
- A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
- A7E9B6C212D37EC400DA6239 /* decalc.h */,
A7E9B74612D37EC400DA6239 /* maligner.h */,
A7E9B74512D37EC400DA6239 /* maligner.cpp */,
+ A7BF221314587886000AD524 /* myPerseus.h */,
+ A7BF221214587886000AD524 /* myPerseus.cpp */,
A7E9B79312D37EC400DA6239 /* pintail.cpp */,
A7E9B79412D37EC400DA6239 /* pintail.h */,
A7E9B82E12D37EC400DA6239 /* slayer.cpp */,
A7E9B68F12D37EC400DA6239 /* classify.h */,
A7E9B73812D37EC400DA6239 /* knn.h */,
A7E9B73712D37EC400DA6239 /* knn.cpp */,
- A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */,
- A7E9B78A12D37EC400DA6239 /* phylodiversity.h */,
A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */,
A7E9B78E12D37EC400DA6239 /* phylosummary.h */,
A7E9B78F12D37EC400DA6239 /* phylotree.cpp */,
A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */,
A7E9B7B512D37EC400DA6239 /* readcolumn.h */,
A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */,
- A7E9B7B912D37EC400DA6239 /* readotu.cpp */,
- A7E9B7BA12D37EC400DA6239 /* readotu.h */,
A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */,
A7E9B7BE12D37EC400DA6239 /* readphylip.h */,
A7E9B7BF12D37EC400DA6239 /* readtree.cpp */,
A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
+ A7D755D71535F665009BF21A /* treereader.h */,
+ A7D755D91535F679009BF21A /* treereader.cpp */,
);
name = read;
sourceTree = "<group>";
A7E9BA5612D39BD800DA6239 /* metastats */ = {
isa = PBXGroup;
children = (
- A7E9B75512D37EC400DA6239 /* metastats.h */,
- A7E9B75612D37EC400DA6239 /* metastats2.c */,
+ A7D161E7149F7F50000523E8 /* fortran */,
+ A79234D513C74BF6002B08E2 /* mothurfisher.h */,
+ A79234D613C74BF6002B08E2 /* mothurfisher.cpp */,
+ A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */,
+ A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */,
+ A74A9A9D148E881E00AB5E3E /* spline.h */,
+ A74A9A9E148E881E00AB5E3E /* spline.cpp */,
);
name = metastats;
sourceTree = "<group>";
8DD76FAF0486AB0100D96B5E /* CopyFiles */,
);
buildRules = (
+ A7D162CB149F96CA000523E8 /* PBXBuildRule */,
);
dependencies = (
);
08FB7793FE84155DC02AAC07 /* Project object */ = {
isa = PBXProject;
attributes = {
+ LastUpgradeCheck = 0420;
ORGANIZATIONNAME = "Schloss Lab";
};
- buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */;
- compatibilityVersion = "Xcode 3.1";
+ buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
+ compatibilityVersion = "Xcode 3.2";
developmentRegion = English;
hasScannedForEncodings = 1;
knownRegions = (
A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */,
A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */,
A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */,
- A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */,
A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */,
A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */,
A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */,
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 */,
A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */,
A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */,
A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */,
- A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */,
+ A7E9B8B312D37EC400DA6239 /* consensus.cpp in Sources */,
A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */,
A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */,
A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */,
A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */,
A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */,
A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */,
- A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */,
A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */,
A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */,
A7E9B8CA12D37EC400DA6239 /* formatphylip.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 */,
A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */,
A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */,
A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */,
- A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */,
A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */,
A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */,
A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */,
A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */,
A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */,
- A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */,
A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */,
A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */,
A7E9B91912D37EC400DA6239 /* phylotree.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 */,
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 */,
+ A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */,
+ A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */,
+ A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */,
+ A721765713BB9F7D0014DAAE /* referencedb.cpp in Sources */,
+ A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */,
+ A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */,
+ A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */,
+ A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */,
+ A7FF19F2140FFDA500AD216D /* trimoligos.cpp in Sources */,
+ A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */,
+ A7FFB558142CA02C004884F2 /* summarytaxcommand.cpp in Sources */,
+ A7BF221414587886000AD524 /* myPerseus.cpp in Sources */,
+ A7BF2232145879B2000AD524 /* chimeraperseuscommand.cpp in Sources */,
+ A774101414695AF60098E6AC /* shhhseqscommand.cpp in Sources */,
+ A774104814696F320098E6AC /* myseqdist.cpp in Sources */,
+ A77410F614697C300098E6AC /* seqnoise.cpp in Sources */,
+ A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */,
+ A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */,
+ A7FA2AC714A0E881007C09A6 /* bsplvb.f in Sources */,
+ A7FA2AC814A0E881007C09A6 /* bsplvd.f in Sources */,
+ A7FA2AC914A0E881007C09A6 /* bvalue.f in Sources */,
+ A7FA2ACA14A0E881007C09A6 /* daxpy.f in Sources */,
+ A7FA2ACB14A0E881007C09A6 /* ddot.f in Sources */,
+ A7FA2ACC14A0E881007C09A6 /* dpbfa.f in Sources */,
+ A7FA2ACD14A0E881007C09A6 /* dpbsl.f in Sources */,
+ A7FA2ACE14A0E881007C09A6 /* interv.f in Sources */,
+ A7FA2ACF14A0E881007C09A6 /* sgram.f in Sources */,
+ A7FA2AD014A0E881007C09A6 /* sinerp.f in Sources */,
+ A7FA2AD114A0E881007C09A6 /* stxwx.f in Sources */,
+ A7FA2B1614A0EBEA007C09A6 /* sslvrg.f in Sources */,
+ A7FA2B5B14A0F0C2007C09A6 /* intrv.f in Sources */,
+ A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */,
+ A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */,
+ A7EEB0F514F29BFE00344B83 /* classifytreecommand.cpp in Sources */,
+ A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */,
+ A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */,
+ A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */,
+ A77EBD2F1523709100ED407C /* createdatabasecommand.cpp in Sources */,
+ A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */,
+ A7D755DA1535F679009BF21A /* treereader.cpp in Sources */,
+ A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
ALWAYS_SEARCH_USER_PATHS = NO;
COPY_PHASE_STRIP = NO;
GCC_DYNAMIC_NO_PIC = NO;
- GCC_ENABLE_FIX_AND_CONTINUE = YES;
GCC_MODEL_TUNING = G5;
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 = 3;
+ GCC_ENABLE_SSE3_EXTENSIONS = NO;
+ GCC_ENABLE_SSE41_EXTENSIONS = NO;
+ GCC_ENABLE_SSE42_EXTENSIONS = NO;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"MOTHUR_FILES=\"\\\"../release\\\"\"",
- "VERSION=\"\\\"1.16.0\\\"\"",
- "RELEASE_DATE=\"\\\"2/7/2011\\\"\"",
+ "VERSION=\"\\\"1.24.0\\\"\"",
+ "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
);
+ "GCC_VERSION[arch=*]" = "";
GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
GCC_WARN_UNUSED_VARIABLE = YES;
+ HEADER_SEARCH_PATHS = "";
INSTALL_PATH = "";
MACH_O_TYPE = mh_execute;
ONLY_ACTIVE_ARCH = YES;
OTHER_CPLUSPLUSFLAGS = (
- "-DUSE_READLINE",
"-DBIT_VERSION",
+ "-DUSE_READLINE",
"$(OTHER_CFLAGS)",
);
OTHER_LDFLAGS = (
"-lncurses",
"-lreadline",
);
- PREBINDING = NO;
- SDKROOT = macosx10.5;
+ SDKROOT = macosx10.6;
+ USER_HEADER_SEARCH_PATHS = "";
};
name = Debug;
};
1DEB928B08733DD80010E9CD /* Release */ = {
isa = XCBuildConfiguration;
buildSettings = {
- ARCHS = "$(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_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
- "MOTHUR_FILES=\"\\\"../release\\\"\"",
- "VERSION=\"\\\"1.15.0\\\"\"",
- "RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
+ "VERSION=\"\\\"1.25.0\\\"\"",
+ "RELEASE_DATE=\"\\\"4/30/2012\\\"\"",
);
GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
GCC_WARN_ABOUT_RETURN_TYPE = YES;
"-lncurses",
"-lreadline",
);
- PREBINDING = NO;
- SDKROOT = macosx10.5;
+ SDKROOT = macosx10.6;
};
name = Release;
};
defaultConfigurationIsVisible = 0;
defaultConfigurationName = Release;
};
- 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
+ 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
isa = XCConfigurationList;
buildConfigurations = (
1DEB928A08733DD80010E9CD /* Debug */,
projects / mothur.git / blobdiff