msa source listing

cleanup.win

NAMESPACE

DESCRIPTION

cleanup

build/vignette.rds

src/SplitCharVector2List.cpp

src/Makevars.win

src/SplitCharVector2List.h

src/SplitCharVector2Matrix.h

src/R_init_msa.cpp

src/Makevars

src/SplitCharVector2Matrix.cpp

src/ClustalW/depcomp

src/ClustalW/config.guess

src/ClustalW/configure.ac

src/ClustalW/msaMakefile.win

src/ClustalW/Makefile.in

src/ClustalW/COPYING.LESSER

src/ClustalW/Makefile.am

src/ClustalW/COPYING

src/ClustalW/clustalw_help

src/ClustalW/configure

src/ClustalW/config.sub

src/ClustalW/install-sh

src/ClustalW/msaMakefile

src/ClustalW/missing

src/ClustalW/aclocal.m4

src/ClustalW/src/clustalw_version.h.in

src/ClustalW/src/Clustal.cpp

src/ClustalW/src/RClustalWMain.h

src/ClustalW/src/RClustalW.h

src/ClustalW/src/Makefile.in

src/ClustalW/src/Makefile.am

src/ClustalW/src/RClustalW.cpp

src/ClustalW/src/Clustal.h

src/ClustalW/src/Help.h

src/ClustalW/src/main.cpp

src/ClustalW/src/RClustalWMain.cpp

src/ClustalW/src/clustalw_version.h

src/ClustalW/src/config.h.in

src/ClustalW/src/Help.cpp

src/ClustalW/src/tree/UnRootedClusterTree.cpp

src/ClustalW/src/tree/ClusterTreeOutput.cpp

src/ClustalW/src/tree/AlignmentSteps.h

src/ClustalW/src/tree/TreeInterface.cpp

src/ClustalW/src/tree/ClusterTreeOutput.h

src/ClustalW/src/tree/ClusterTree.cpp

src/ClustalW/src/tree/Tree.cpp

src/ClustalW/src/tree/TreeInterface.h

src/ClustalW/src/tree/NJTree.cpp

src/ClustalW/src/tree/ClusterTreeAlgorithm.h

src/ClustalW/src/tree/NJTree.h

src/ClustalW/src/tree/RandomGenerator.h

src/ClustalW/src/tree/AlignmentSteps.cpp

src/ClustalW/src/tree/dayhoff.h

src/ClustalW/src/tree/Tree.h

src/ClustalW/src/tree/ClusterTree.h

src/ClustalW/src/tree/RandomGenerator.cpp

src/ClustalW/src/tree/UnRootedClusterTree.h

src/ClustalW/src/tree/UPGMA/RootedGuideTree.h

src/ClustalW/src/tree/UPGMA/RootedTreeOutput.cpp

src/ClustalW/src/tree/UPGMA/UPGMAAlgorithm.cpp

src/ClustalW/src/tree/UPGMA/RootedClusterTree.cpp

src/ClustalW/src/tree/UPGMA/UPGMAAlgorithm.h

src/ClustalW/src/tree/UPGMA/RootedGuideTree.cpp

src/ClustalW/src/tree/UPGMA/RootedTreeOutput.h

src/ClustalW/src/tree/UPGMA/upgmadata.h

src/ClustalW/src/tree/UPGMA/Node.cpp

src/ClustalW/src/tree/UPGMA/Node.h

src/ClustalW/src/tree/UPGMA/RootedClusterTree.h

src/ClustalW/src/multipleAlign/ProfileBase.h

src/ClustalW/src/multipleAlign/ProfileStandard.h

src/ClustalW/src/multipleAlign/ProfileWithSub.cpp

src/ClustalW/src/multipleAlign/MyersMillerProfileAlign.cpp

src/ClustalW/src/multipleAlign/ProfileAlignAlgorithm.h

src/ClustalW/src/multipleAlign/Iteration.h

src/ClustalW/src/multipleAlign/ProfileBase.cpp

src/ClustalW/src/multipleAlign/ProfileStandard.cpp

src/ClustalW/src/multipleAlign/MyersMillerProfileAlign.h

src/ClustalW/src/multipleAlign/MSA.cpp

src/ClustalW/src/multipleAlign/ProfileWithSub.h

src/ClustalW/src/multipleAlign/LowScoreSegProfile.cpp

src/ClustalW/src/multipleAlign/LowScoreSegProfile.h

src/ClustalW/src/multipleAlign/Iteration.cpp

src/ClustalW/src/multipleAlign/MSA.h

src/ClustalW/src/pairwise/PairwiseAlignBase.h

src/ClustalW/src/pairwise/FastPairwiseAlign.cpp

src/ClustalW/src/pairwise/FullPairwiseAlign.h

src/ClustalW/src/pairwise/FullPairwiseAlign.cpp

src/ClustalW/src/pairwise/FastPairwiseAlign.h

src/ClustalW/src/alignment/AlignmentOutput.cpp

src/ClustalW/src/alignment/Alignment.cpp

src/ClustalW/src/alignment/Alignment.h

src/ClustalW/src/alignment/AlignmentOutput.h

src/ClustalW/src/alignment/ObjectiveScore.h

src/ClustalW/src/alignment/ObjectiveScore.cpp

src/ClustalW/src/alignment/Sequence.cpp

src/ClustalW/src/alignment/Sequence.h

src/ClustalW/src/fileInput/FileParser.cpp

src/ClustalW/src/fileInput/MSFFileParser.cpp

src/ClustalW/src/fileInput/GDEFileParser.h

src/ClustalW/src/fileInput/MSFFileParser.h

src/ClustalW/src/fileInput/RSFFileParser.cpp

src/ClustalW/src/fileInput/PearsonFileParser.cpp

src/ClustalW/src/fileInput/ClustalFileParser.h

src/ClustalW/src/fileInput/PearsonFileParser.h

src/ClustalW/src/fileInput/PIRFileParser.h

src/ClustalW/src/fileInput/PIRFileParser.cpp

src/ClustalW/src/fileInput/InFileStream.h

src/ClustalW/src/fileInput/InFileStream.cpp

src/ClustalW/src/fileInput/FileReader.cpp

src/ClustalW/src/fileInput/FileReader.h

src/ClustalW/src/fileInput/FileParser.h

src/ClustalW/src/fileInput/EMBLFileParser.h

src/ClustalW/src/fileInput/RSFFileParser.h

src/ClustalW/src/fileInput/GDEFileParser.cpp

src/ClustalW/src/fileInput/ClustalFileParser.cpp

src/ClustalW/src/fileInput/EMBLFileParser.cpp

src/ClustalW/src/interface/CommandLineParser.h

src/ClustalW/src/interface/InteractiveMenu.cpp

src/ClustalW/src/interface/InteractiveMenu.h

src/ClustalW/src/interface/CommandLineParser.cpp

src/ClustalW/src/substitutionMatrix/SubMatrix.h

src/ClustalW/src/substitutionMatrix/matrices.h

src/ClustalW/src/substitutionMatrix/SubMatrix.cpp

src/ClustalW/src/substitutionMatrix/globalmatrix.h

src/ClustalW/src/general/ClustalWResources.h

src/ClustalW/src/general/debuglogObject.h

src/ClustalW/src/general/OutputFile.h

src/ClustalW/src/general/InvalidCombination.cpp

src/ClustalW/src/general/VectorOutOfRange.cpp

src/ClustalW/src/general/RandomAccessLList.h

src/ClustalW/src/general/Array2D.h

src/ClustalW/src/general/userparams.h

src/ClustalW/src/general/DebugLog.h

src/ClustalW/src/general/Stats.h

src/ClustalW/src/general/Utility.cpp

src/ClustalW/src/general/clustalw.h

src/ClustalW/src/general/Utility.h

src/ClustalW/src/general/statsObject.h

src/ClustalW/src/general/param.h

src/ClustalW/src/general/SquareMat.h

src/ClustalW/src/general/VectorUtility.h

src/ClustalW/src/general/ClustalWResources.cpp

src/ClustalW/src/general/SequenceNotFoundException.h

src/ClustalW/src/general/SymMatrix.h

src/ClustalW/src/general/VectorOutOfRange.h

src/ClustalW/src/general/OutputFile.cpp

src/ClustalW/src/general/UserParameters.h

src/ClustalW/src/general/DebugLog.cpp

src/ClustalW/src/general/general.h

src/ClustalW/src/general/Stats.cpp

src/ClustalW/src/general/UserParameters.cpp

src/ClustalW/src/general/utils.h

src/ClustalW/src/general/SymMatrix.cpp

src/ClustalW/windows/Makefile

src/ClustalW/windows/src/clustalw_version.h

src/ClustalW/windows/src/Makefile

src/ClustalW/windows/src/config.h

src/ClustalW/windows/m4/Makefile

src/ClustalW/m4/Makefile.in

src/ClustalW/m4/Makefile.am

src/Muscle/dpreglist.cpp

src/Muscle/threewaywt.cpp

src/Muscle/treefrommsa.cpp

src/Muscle/make.err

src/Muscle/estring.h

src/Muscle/termgaps.cpp

src/Muscle/estring.cpp

src/Muscle/alpha.h

src/Muscle/setgscweights.cpp

src/Muscle/objscore.cpp

src/Muscle/bittraceback.cpp

src/Muscle/distcalc.h

src/Muscle/sptest.cpp

src/Muscle/nucmx.cpp

src/Muscle/phyfromclust.cpp

src/Muscle/dpregionlist.h

src/Muscle/glbalign.cpp

src/Muscle/edgelist.h

src/Muscle/muscle.cpp

src/Muscle/pwpath.cpp

src/Muscle/difftreese.cpp

src/Muscle/usage.cpp

src/Muscle/setnewhandler.cpp

src/Muscle/gatest.cpp

src/Muscle/RMuscle.cpp

src/Muscle/profile.cpp

src/Muscle/msadist.h

src/Muscle/pam200mafft.cpp

src/Muscle/blosum62.cpp

src/Muscle/typetostr.cpp

src/Muscle/savebest.cpp

src/Muscle/edgelist.cpp

src/Muscle/glbalndimer.cpp

src/Muscle/refine.cpp

src/Muscle/scorehistory.h

src/Muscle/domuscle.cpp

src/Muscle/msaMakefile.win

src/Muscle/tomhydro.cpp

src/Muscle/stabilize.cpp

src/Muscle/traceback.cpp

src/Muscle/distfunc.h

src/Muscle/henikoffweightpb.cpp

src/Muscle/fastclust.cpp

src/Muscle/progalign.cpp

src/Muscle/RMuscle.h

src/Muscle/svnversion.h

src/Muscle/refinetreee.cpp

src/Muscle/phy4.cpp

src/Muscle/gonnet.h

src/Muscle/seq.cpp

src/Muscle/scoremx.cpp

src/Muscle/fasta.cpp

src/Muscle/nwdasimple.cpp

src/Muscle/outweights.cpp

src/Muscle/globalsother.cpp

src/Muscle/params.h

src/Muscle/subfams.cpp

src/Muscle/cluster.cpp

src/Muscle/glbalignle.cpp

src/Muscle/cons.cpp

src/Muscle/phytofile.cpp

src/Muscle/fastdistkmer.cpp

src/Muscle/options.cpp

src/Muscle/types.h

src/Muscle/globals.cpp

src/Muscle/globalswin32.cpp

src/Muscle/globalslinux.cpp

src/Muscle/clustsetdf.h

src/Muscle/difftrees.cpp

src/Muscle/writescorefile.cpp

src/Muscle/physeq.cpp

src/Muscle/profile.h

src/Muscle/finddiagsn.cpp

src/Muscle/diaglist.cpp

src/Muscle/msa2.cpp

src/Muscle/subfam.cpp

src/Muscle/realigndiffse.cpp

src/Muscle/glbalignss.cpp

src/Muscle/unixio.h

src/Muscle/distfunc.cpp

src/Muscle/glbaligndiag.cpp

src/Muscle/clwwt.cpp

src/Muscle/gotowt.cpp

src/Muscle/muscle.h

src/Muscle/distcalc.cpp

src/Muscle/muscleout.cpp

src/Muscle/tree.h

src/Muscle/glbalignla.cpp

src/Muscle/clust.h

src/Muscle/glbalignsimple.cpp

src/Muscle/clust.cpp

src/Muscle/vtml2.cpp

src/Muscle/validateids.cpp

src/Muscle/alpha.cpp

src/Muscle/mhack.cpp

src/Muscle/glbalignns.cpp

src/Muscle/textfile.h

src/Muscle/diffobjscore.cpp

src/Muscle/distpwkimura.cpp

src/Muscle/enumtostr.cpp

src/Muscle/params.cpp

src/Muscle/pwpath.h

src/Muscle/glbalignspn.cpp

src/Muscle/ppscore.cpp

src/Muscle/seqvect.cpp

src/Muscle/phyfromfile.cpp

src/Muscle/profdb.cpp

src/Muscle/tracebacksw.cpp

src/Muscle/local.cpp

src/Muscle/version.txt

src/Muscle/profilefrommsa.cpp

src/Muscle/phy3.cpp

src/Muscle/makerootmsab.cpp

src/Muscle/README.txt

src/Muscle/main.cpp

src/Muscle/color.cpp

src/Muscle/nwdasmall.cpp

src/Muscle/blosumla.cpp

src/Muscle/objscoreda.cpp

src/Muscle/timing.h

src/Muscle/msadistkimura.h

src/Muscle/readmx.cpp

src/Muscle/refinetree.cpp

src/Muscle/html.cpp

src/Muscle/fastdistnuc.cpp

src/Muscle/msa.h

src/Muscle/fastdistjones.cpp

src/Muscle/glbalign352.cpp

src/Muscle/fastdistkbit.cpp

src/Muscle/intmath.cpp

src/Muscle/objscore.h

src/Muscle/msa.cpp

src/Muscle/spfast.cpp

src/Muscle/clustsetmsa.h

src/Muscle/seqvect.h

src/Muscle/phy.cpp

src/Muscle/refinehoriz.cpp

src/Muscle/tracebackopt.cpp

src/Muscle/progressivealign.cpp

src/Muscle/onexception.cpp

src/Muscle/drawtree.cpp

src/Muscle/msf.cpp

src/Muscle/fasta2.cpp

src/Muscle/dpreglist.h

src/Muscle/redblack.cpp

src/Muscle/aligntwoprofs.cpp

src/Muscle/fastdist.cpp

src/Muscle/objscore2.cpp

src/Muscle/mpam200.cpp

src/Muscle/upgma2.cpp

src/Muscle/textfile.cpp

src/Muscle/make.out

src/Muscle/refinesubfams.cpp

src/Muscle/progress.cpp

src/Muscle/Makefile

src/Muscle/refinew.cpp

src/Muscle/diaglist.h

src/Muscle/setblosumweights.cpp

src/Muscle/msadistmafft.h

src/Muscle/fastscorepath2.cpp

src/Muscle/enumopts.cpp

src/Muscle/maketree.cpp

src/Muscle/fastdistmafft.cpp

src/Muscle/aligngivenpath.cpp

src/Muscle/mk

src/Muscle/aln.cpp

src/Muscle/enums.h

src/Muscle/scoregaps.cpp

src/Muscle/finddiags.cpp

src/Muscle/msaMakefile

src/Muscle/seq.h

src/Muscle/scoredist.cpp

src/Muscle/releases.txt

src/Muscle/gonnet.cpp

src/Muscle/refinevert.cpp

src/Muscle/sw.cpp

src/Muscle/phy2.cpp

src/Muscle/posgap.cpp

src/Muscle/dosp.cpp

src/Muscle/hydro.cpp

src/Muscle/diffpaths.cpp

src/Muscle/nwrec.cpp

src/Muscle/cluster.h

src/Muscle/enumopts.h

src/Muscle/realigndiffs.cpp

src/Muscle/makerootmsa.cpp

src/Muscle/nwsmall.cpp

src/Muscle/glbalignsp.cpp

src/Muscle/aligntwomsas.cpp

src/Muscle/gapscoredimer.h

src/Muscle/svnmods.h

src/Muscle/msadistkimura.cpp

src/Muscle/henikoffweight.cpp

src/Muscle/anchors.cpp

src/Muscle/globalsosx.cpp

src/Muscle/scorepp.cpp

src/Muscle/intmath.h

src/Muscle/nwdasimple2.cpp

src/Muscle/scorehistory.cpp

src/Muscle/aligngivenpathsw.cpp

src/Muscle/clustset.h

src/gc-7.2/depcomp

src/gc-7.2/config.guess

src/gc-7.2/darwin_stop_world.c

src/gc-7.2/SMakefile.amiga

src/gc-7.2/misc.c

src/gc-7.2/gc.mak

src/gc-7.2/mkinstalldirs

src/gc-7.2/obj_map.c

src/gc-7.2/dbg_mlc.c

src/gc-7.2/allchblk.c

src/gc-7.2/reclaim.c

src/gc-7.2/configure.ac

src/gc-7.2/ChangeLog

src/gc-7.2/mark.c

src/gc-7.2/CMakeLists.txt

src/gc-7.2/msaMakefile.win

src/gc-7.2/Makefile.in

src/gc-7.2/blacklst.c

src/gc-7.2/callprocs

src/gc-7.2/gc_dlopen.c

src/gc-7.2/stubborn.c

src/gc-7.2/malloc.c

src/gc-7.2/gc_cpp.cc

src/gc-7.2/Makefile.am

src/gc-7.2/checksums.c

src/gc-7.2/MacProjects.sit.hqx

src/gc-7.2/ltmain.sh

src/gc-7.2/alloc.c

src/gc-7.2/gc_cpp.cpp

src/gc-7.2/backgraph.c

src/gc-7.2/pthread_stop_world.c

src/gc-7.2/real_malloc.c

src/gc-7.2/new_hblk.c

src/gc-7.2/bdw-gc.pc.in

src/gc-7.2/README.QUICK

src/gc-7.2/headers.c

src/gc-7.2/finalize.c

src/gc-7.2/configure

src/gc-7.2/specific.c

src/gc-7.2/compile

src/gc-7.2/config.sub

src/gc-7.2/test-driver

src/gc-7.2/pthread_support.c

src/gc-7.2/gcj_mlc.c

src/gc-7.2/BCC_MAKEFILE

src/gc-7.2/NT_X64_THREADS_MAKEFILE

src/gc-7.2/Makefile.DLLs

src/gc-7.2/pcr_interface.c

src/gc-7.2/NT_STATIC_THREADS_MAKEFILE

src/gc-7.2/WCC_MAKEFILE

src/gc-7.2/install-sh

src/gc-7.2/dyn_load.c

src/gc-7.2/win32_threads.c

src/gc-7.2/PCR-Makefile

src/gc-7.2/OS2_MAKEFILE

src/gc-7.2/mach_dep.c

src/gc-7.2/typd_mlc.c

src/gc-7.2/configure.host

src/gc-7.2/build_atomic_ops.sh

src/gc-7.2/mallocx.c

src/gc-7.2/thread_local_alloc.c

src/gc-7.2/digimars.mak

src/gc-7.2/Makefile.direct

src/gc-7.2/autogen.sh

src/gc-7.2/EMX_MAKEFILE

src/gc-7.2/msaMakefile

src/gc-7.2/missing

src/gc-7.2/build_atomic_ops.sh.cygwin

src/gc-7.2/mark_rts.c

src/gc-7.2/NT_X64_STATIC_THREADS_MAKEFILE

src/gc-7.2/ptr_chck.c

src/gc-7.2/pthread_start.c

src/gc-7.2/aclocal.m4

src/gc-7.2/NT_MAKEFILE

src/gc-7.2/os_dep.c

src/gc-7.2/Makefile.dj

src/gc-7.2/doc/simple_example.html

src/gc-7.2/doc/gcinterface.html

src/gc-7.2/doc/README.amiga

src/gc-7.2/doc/README.hp

src/gc-7.2/doc/debugging.html

src/gc-7.2/doc/barrett_diagram

src/gc-7.2/doc/README.sgi

src/gc-7.2/doc/README.MacOSX

src/gc-7.2/doc/overview.html

src/gc-7.2/doc/README.cmake

src/gc-7.2/doc/README.OS2

src/gc-7.2/doc/README.cords

src/gc-7.2/doc/README.DGUX386

src/gc-7.2/doc/README.macros

src/gc-7.2/doc/README.environment

src/gc-7.2/doc/README.dj

src/gc-7.2/doc/README.Mac

src/gc-7.2/doc/README.uts

src/gc-7.2/doc/gc.man

src/gc-7.2/doc/README.win64

src/gc-7.2/doc/doc.am

src/gc-7.2/doc/README.rs6000

src/gc-7.2/doc/scale.html

src/gc-7.2/doc/tree.html

src/gc-7.2/doc/porting.html

src/gc-7.2/doc/README.win32

src/gc-7.2/doc/leak.html

src/gc-7.2/doc/README.changes

src/gc-7.2/doc/README

src/gc-7.2/doc/README.linux

src/gc-7.2/doc/README.darwin

src/gc-7.2/doc/README.contributors

src/gc-7.2/doc/README.ews4800

src/gc-7.2/doc/gcdescr.html

src/gc-7.2/doc/README.arm.cross

src/gc-7.2/doc/README.autoconf

src/gc-7.2/doc/README.solaris2

src/gc-7.2/include/gc_amiga_redirects.h

src/gc-7.2/include/gc_backptr.h

src/gc-7.2/include/leak_detector.h

src/gc-7.2/include/gc_cpp.h

src/gc-7.2/include/gc_mark.h

src/gc-7.2/include/weakpointer.h

src/gc-7.2/include/include.am

src/gc-7.2/include/gc_tiny_fl.h

src/gc-7.2/include/gc.h

src/gc-7.2/include/gc_config_macros.h

src/gc-7.2/include/gc_allocator.h

src/gc-7.2/include/ec.h

src/gc-7.2/include/gc_pthread_redirects.h

src/gc-7.2/include/gc_typed.h

src/gc-7.2/include/cord.h

src/gc-7.2/include/gc_gcj.h

src/gc-7.2/include/javaxfc.h

src/gc-7.2/include/gc_inline.h

src/gc-7.2/include/gc_version.h

src/gc-7.2/include/new_gc_alloc.h

src/gc-7.2/include/extra/gc_cpp.h

src/gc-7.2/include/extra/gc.h

src/gc-7.2/include/private/cord_pos.h

src/gc-7.2/include/private/darwin_semaphore.h

src/gc-7.2/include/private/thread_local_alloc.h

src/gc-7.2/include/private/darwin_stop_world.h

src/gc-7.2/include/private/pthread_support.h

src/gc-7.2/include/private/gc_locks.h

src/gc-7.2/include/private/gcconfig.h

src/gc-7.2/include/private/dbg_mlc.h

src/gc-7.2/include/private/gc_priv.h

src/gc-7.2/include/private/gc_pmark.h

src/gc-7.2/include/private/msvc_dbg.h

src/gc-7.2/include/private/config.h.in

src/gc-7.2/include/private/gc_hdrs.h

src/gc-7.2/include/private/pthread_stop_world.h

src/gc-7.2/include/private/specific.h

src/gc-7.2/extra/add_gc_prefix.c

src/gc-7.2/extra/AmigaOS.c

src/gc-7.2/extra/msvc_dbg.c

src/gc-7.2/extra/setjmp_t.c

src/gc-7.2/extra/if_mach.c

src/gc-7.2/extra/gcname.c

src/gc-7.2/extra/threadlibs.c

src/gc-7.2/extra/if_not_there.c

src/gc-7.2/extra/gc.c

src/gc-7.2/extra/MacOS.c

src/gc-7.2/Mac_files/MacOS_Test_config.h

src/gc-7.2/Mac_files/dataend.c

src/gc-7.2/Mac_files/datastart.c

src/gc-7.2/Mac_files/MacOS_config.h

src/gc-7.2/libatomic_ops/depcomp

src/gc-7.2/libatomic_ops/config.guess

src/gc-7.2/libatomic_ops/mkinstalldirs

src/gc-7.2/libatomic_ops/configure.ac

src/gc-7.2/libatomic_ops/ChangeLog

src/gc-7.2/libatomic_ops/Makefile.in

src/gc-7.2/libatomic_ops/Makefile.am

src/gc-7.2/libatomic_ops/COPYING

src/gc-7.2/libatomic_ops/configure

src/gc-7.2/libatomic_ops/compile

src/gc-7.2/libatomic_ops/config.sub

src/gc-7.2/libatomic_ops/test-driver

src/gc-7.2/libatomic_ops/NEWS

src/gc-7.2/libatomic_ops/install-sh

src/gc-7.2/libatomic_ops/AUTHORS

src/gc-7.2/libatomic_ops/INSTALL

src/gc-7.2/libatomic_ops/README

src/gc-7.2/libatomic_ops/missing

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