msa: Multiple Sequence Alignment

The 'msa' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

AuthorEnrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
Date of publicationNone
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2)
Version1.6.0
http://www.bioinf.jku.at/software/msa/

View on Bioconductor

Functions

class:MsaAAMultipleAlignment Man page
class:MsaDNAMultipleAlignment Man page
class:MsaMetaData Man page
class:MsaRNAMultipleAlignment Man page
msa Man page
MsaAAMultipleAlignment Man page
MsaAAMultipleAlignment-class Man page
msaCheckNames Man page
msaClustalOmega Man page
msaClustalW Man page
msaConvert Man page
MsaDNAMultipleAlignment Man page
MsaDNAMultipleAlignment-class Man page
MsaMetaData Man page
MsaMetaData-class Man page
msaMuscle Man page
msa-package Man page
msaPackage Man page
msaPrettyPrint Man page
MsaRNAMultipleAlignment Man page
MsaRNAMultipleAlignment-class Man page
params,MsaAAMultipleAlignment-method Man page
params,MsaDNAMultipleAlignment-method Man page
params,MsaMetaData-method Man page
params,MsaRNAMultipleAlignment-method Man page
print,MsaAAMultipleAlignment-method Man page
print,MsaDNAMultipleAlignment-method Man page
print,MsaRNAMultipleAlignment-method Man page
show,MsaAAMultipleAlignment-method Man page
show,MsaDNAMultipleAlignment-method Man page
show,MsaRNAMultipleAlignment-method Man page
version Man page
version,MsaAAMultipleAlignment-method Man page
version,MsaDNAMultipleAlignment-method Man page
version,MsaMetaData-method Man page
version,MsaRNAMultipleAlignment-method Man page

Files

msa/DESCRIPTION
msa/NAMESPACE
msa/R
msa/R/AllClasses.R msa/R/AllGenerics.R msa/R/convertRows.R msa/R/helperFunctions.R msa/R/inputChecks.R msa/R/msa.R msa/R/msaCheckNames.R msa/R/msaClustalOmega.R msa/R/msaClustalW.R msa/R/msaConvert.R msa/R/msaMuscle.R msa/R/msaPrettyPrint.R msa/R/params-methods.R msa/R/print-methods.R msa/R/show-methods.R msa/R/version-methods.R
msa/build
msa/build/vignette.rds
msa/cleanup
msa/cleanup.win
msa/inst
msa/inst/CITATION
msa/inst/COPYRIGHT
msa/inst/NEWS
msa/inst/doc
msa/inst/doc/msa.R
msa/inst/doc/msa.Rnw
msa/inst/doc/msa.pdf
msa/inst/examples
msa/inst/examples/HemoglobinAA.fasta
msa/inst/examples/exampleAA.fasta
msa/inst/examples/exampleDNA.fasta
msa/inst/examples/exampleRNA.fasta
msa/inst/extdata
msa/inst/extdata/msaClustalOmegaHelp.txt
msa/inst/extdata/msaClustalWHelp.txt
msa/inst/extdata/msaCommonHelp.txt
msa/inst/extdata/msaHelpPrefix.txt
msa/inst/extdata/msaMuscleHelp.txt
msa/inst/tex
msa/inst/tex/texshade.sty
msa/man
msa/man/MsaMetaData-class.Rd msa/man/MsaMultipleAlignmentClasses.Rd msa/man/msa-package.Rd msa/man/msa.Rd msa/man/msaCheckNames.Rd msa/man/msaClustalOmega.Rd msa/man/msaClustalW.Rd msa/man/msaConvert.Rd msa/man/msaMuscle.Rd msa/man/msaPrettyPrint.Rd
msa/src
msa/src/ClustalOmega
msa/src/ClustalOmega/AUTHORS
msa/src/ClustalOmega/COPYING
msa/src/ClustalOmega/Doxyfile
msa/src/ClustalOmega/Doxyfile.in
msa/src/ClustalOmega/Makefile.am
msa/src/ClustalOmega/Makefile.in
msa/src/ClustalOmega/aclocal.m4
msa/src/ClustalOmega/clustalo.pc.in
msa/src/ClustalOmega/config.guess
msa/src/ClustalOmega/config.sub
msa/src/ClustalOmega/configure
msa/src/ClustalOmega/configure.ac
msa/src/ClustalOmega/depcomp
msa/src/ClustalOmega/install-sh
msa/src/ClustalOmega/ltmain.sh
msa/src/ClustalOmega/m4
msa/src/ClustalOmega/m4/ax_openmp.m4
msa/src/ClustalOmega/m4/ax_prefix_config_h.m4
msa/src/ClustalOmega/m4/libtool.m4
msa/src/ClustalOmega/m4/ltoptions.m4
msa/src/ClustalOmega/m4/ltsugar.m4
msa/src/ClustalOmega/m4/ltversion.m4
msa/src/ClustalOmega/missing
msa/src/ClustalOmega/msaMakefile
msa/src/ClustalOmega/msaMakefile.win
msa/src/ClustalOmega/src
msa/src/ClustalOmega/src/Makefile.am
msa/src/ClustalOmega/src/Makefile.in
msa/src/ClustalOmega/src/RClustalOmega.cpp
msa/src/ClustalOmega/src/RClustalOmega.h
msa/src/ClustalOmega/src/argtable2
msa/src/ClustalOmega/src/argtable2/CMakeLists.txt
msa/src/ClustalOmega/src/argtable2/Makefile.am
msa/src/ClustalOmega/src/argtable2/Makefile.in
msa/src/ClustalOmega/src/argtable2/Makefile.nmake
msa/src/ClustalOmega/src/argtable2/arg_date.c
msa/src/ClustalOmega/src/argtable2/arg_dbl.c
msa/src/ClustalOmega/src/argtable2/arg_end.c
msa/src/ClustalOmega/src/argtable2/arg_file.c
msa/src/ClustalOmega/src/argtable2/arg_int.c
msa/src/ClustalOmega/src/argtable2/arg_lit.c
msa/src/ClustalOmega/src/argtable2/arg_rem.c
msa/src/ClustalOmega/src/argtable2/arg_rex.c
msa/src/ClustalOmega/src/argtable2/arg_str.c
msa/src/ClustalOmega/src/argtable2/argtable2.c
msa/src/ClustalOmega/src/argtable2/argtable2.def
msa/src/ClustalOmega/src/argtable2/argtable2.h
msa/src/ClustalOmega/src/argtable2/config.h
msa/src/ClustalOmega/src/argtable2/config.h.in
msa/src/ClustalOmega/src/argtable2/getopt.c
msa/src/ClustalOmega/src/argtable2/getopt.h
msa/src/ClustalOmega/src/argtable2/getopt1.c
msa/src/ClustalOmega/src/clustal
msa/src/ClustalOmega/src/clustal-omega-config.h
msa/src/ClustalOmega/src/clustal-omega.c
msa/src/ClustalOmega/src/clustal-omega.h
msa/src/ClustalOmega/src/clustal/Makefile.am
msa/src/ClustalOmega/src/clustal/Makefile.in
msa/src/ClustalOmega/src/clustal/hhalign_wrapper.c
msa/src/ClustalOmega/src/clustal/hhalign_wrapper.h
msa/src/ClustalOmega/src/clustal/ktuple_pair.c
msa/src/ClustalOmega/src/clustal/ktuple_pair.h
msa/src/ClustalOmega/src/clustal/list.c
msa/src/ClustalOmega/src/clustal/list.h
msa/src/ClustalOmega/src/clustal/log.c
msa/src/ClustalOmega/src/clustal/log.h
msa/src/ClustalOmega/src/clustal/mbed.c
msa/src/ClustalOmega/src/clustal/mbed.h
msa/src/ClustalOmega/src/clustal/muscle_tree.c
msa/src/ClustalOmega/src/clustal/muscle_tree.h
msa/src/ClustalOmega/src/clustal/muscle_upgma.c
msa/src/ClustalOmega/src/clustal/muscle_upgma.h
msa/src/ClustalOmega/src/clustal/pair_dist.c
msa/src/ClustalOmega/src/clustal/pair_dist.h
msa/src/ClustalOmega/src/clustal/progress.c
msa/src/ClustalOmega/src/clustal/progress.h
msa/src/ClustalOmega/src/clustal/queue.h
msa/src/ClustalOmega/src/clustal/seq.c
msa/src/ClustalOmega/src/clustal/seq.h
msa/src/ClustalOmega/src/clustal/symmatrix.c
msa/src/ClustalOmega/src/clustal/symmatrix.h
msa/src/ClustalOmega/src/clustal/tree.c
msa/src/ClustalOmega/src/clustal/tree.h
msa/src/ClustalOmega/src/clustal/util.c
msa/src/ClustalOmega/src/clustal/util.h
msa/src/ClustalOmega/src/clustal/weights.c
msa/src/ClustalOmega/src/clustal/weights.h
msa/src/ClustalOmega/src/clustalo-api-test.c
msa/src/ClustalOmega/src/config.h.in
msa/src/ClustalOmega/src/exceptions4c
msa/src/ClustalOmega/src/exceptions4c/Makefile.am
msa/src/ClustalOmega/src/exceptions4c/Makefile.in
msa/src/ClustalOmega/src/exceptions4c/config.h
msa/src/ClustalOmega/src/exceptions4c/config.h.in
msa/src/ClustalOmega/src/exceptions4c/e4c_lite.c
msa/src/ClustalOmega/src/exceptions4c/e4c_lite.h
msa/src/ClustalOmega/src/hhalign
msa/src/ClustalOmega/src/hhalign/Makefile.am
msa/src/ClustalOmega/src/hhalign/Makefile.in
msa/src/ClustalOmega/src/hhalign/general.h
msa/src/ClustalOmega/src/hhalign/hash-C.h
msa/src/ClustalOmega/src/hhalign/hash.h
msa/src/ClustalOmega/src/hhalign/hhalign.cpp
msa/src/ClustalOmega/src/hhalign/hhalign.h
msa/src/ClustalOmega/src/hhalign/hhalignment-C.h
msa/src/ClustalOmega/src/hhalign/hhalignment.h
msa/src/ClustalOmega/src/hhalign/hhdecl-C.h
msa/src/ClustalOmega/src/hhalign/hhfullalignment-C.h
msa/src/ClustalOmega/src/hhalign/hhfullalignment.h
msa/src/ClustalOmega/src/hhalign/hhfunc-C.h
msa/src/ClustalOmega/src/hhalign/hhfunc.h
msa/src/ClustalOmega/src/hhalign/hhhalfalignment-C.h
msa/src/ClustalOmega/src/hhalign/hhhalfalignment.h
msa/src/ClustalOmega/src/hhalign/hhhit-C.h
msa/src/ClustalOmega/src/hhalign/hhhit.h
msa/src/ClustalOmega/src/hhalign/hhhitlist-C.h
msa/src/ClustalOmega/src/hhalign/hhhitlist.h
msa/src/ClustalOmega/src/hhalign/hhhmm-C.h
msa/src/ClustalOmega/src/hhalign/hhhmm.h
msa/src/ClustalOmega/src/hhalign/hhmatrices-C.h
msa/src/ClustalOmega/src/hhalign/hhutil-C.h
msa/src/ClustalOmega/src/hhalign/list-C.h
msa/src/ClustalOmega/src/hhalign/list.h
msa/src/ClustalOmega/src/hhalign/util-C.h
msa/src/ClustalOmega/src/kmpp
msa/src/ClustalOmega/src/kmpp/KMeans.cpp
msa/src/ClustalOmega/src/kmpp/KMeans.h
msa/src/ClustalOmega/src/kmpp/KmTree.cpp
msa/src/ClustalOmega/src/kmpp/KmTree.h
msa/src/ClustalOmega/src/kmpp/KmUtils.cpp
msa/src/ClustalOmega/src/kmpp/KmUtils.h
msa/src/ClustalOmega/src/kmpp/Makefile.am
msa/src/ClustalOmega/src/kmpp/Makefile.in
msa/src/ClustalOmega/src/main.cpp
msa/src/ClustalOmega/src/mymain.c
msa/src/ClustalOmega/src/mymain.h
msa/src/ClustalOmega/src/squid
msa/src/ClustalOmega/src/squid/00README
msa/src/ClustalOmega/src/squid/COPYRIGHT
msa/src/ClustalOmega/src/squid/LICENSE
msa/src/ClustalOmega/src/squid/Makefile.am
msa/src/ClustalOmega/src/squid/Makefile.in
msa/src/ClustalOmega/src/squid/a2m.c
msa/src/ClustalOmega/src/squid/aligneval.c
msa/src/ClustalOmega/src/squid/alignio.c
msa/src/ClustalOmega/src/squid/clustal.c
msa/src/ClustalOmega/src/squid/clustalo.README
msa/src/ClustalOmega/src/squid/cluster.c
msa/src/ClustalOmega/src/squid/dayhoff.c
msa/src/ClustalOmega/src/squid/eps.c
msa/src/ClustalOmega/src/squid/file.c
msa/src/ClustalOmega/src/squid/getopt.c
msa/src/ClustalOmega/src/squid/gki.c
msa/src/ClustalOmega/src/squid/gki.h
msa/src/ClustalOmega/src/squid/gsi.c
msa/src/ClustalOmega/src/squid/gsi.h
msa/src/ClustalOmega/src/squid/gsi64.c
msa/src/ClustalOmega/src/squid/gsi64.h
msa/src/ClustalOmega/src/squid/hsregex.c
msa/src/ClustalOmega/src/squid/iupac.c
msa/src/ClustalOmega/src/squid/msa.c
msa/src/ClustalOmega/src/squid/msa.h
msa/src/ClustalOmega/src/squid/msf.c
msa/src/ClustalOmega/src/squid/phylip.c
msa/src/ClustalOmega/src/squid/revcomp.c
msa/src/ClustalOmega/src/squid/rk.c
msa/src/ClustalOmega/src/squid/rk.h
msa/src/ClustalOmega/src/squid/selex.c
msa/src/ClustalOmega/src/squid/seqencode.c
msa/src/ClustalOmega/src/squid/shuffle.c
msa/src/ClustalOmega/src/squid/sqerror.c
msa/src/ClustalOmega/src/squid/sqfuncs.h
msa/src/ClustalOmega/src/squid/sqio.c
msa/src/ClustalOmega/src/squid/squid-1.9g.tar.gz
msa/src/ClustalOmega/src/squid/squid.h
msa/src/ClustalOmega/src/squid/squidcore.c
msa/src/ClustalOmega/src/squid/sre_ctype.c
msa/src/ClustalOmega/src/squid/sre_math.c
msa/src/ClustalOmega/src/squid/sre_random.c
msa/src/ClustalOmega/src/squid/sre_random.h
msa/src/ClustalOmega/src/squid/sre_string.c
msa/src/ClustalOmega/src/squid/ssi.c
msa/src/ClustalOmega/src/squid/ssi.h
msa/src/ClustalOmega/src/squid/stack.c
msa/src/ClustalOmega/src/squid/stockholm.c
msa/src/ClustalOmega/src/squid/stockholm.h
msa/src/ClustalOmega/src/squid/stopwatch.c
msa/src/ClustalOmega/src/squid/stopwatch.h
msa/src/ClustalOmega/src/squid/translate.c
msa/src/ClustalOmega/src/squid/types.c
msa/src/ClustalOmega/src/squid/vectorops.c
msa/src/ClustalOmega/src/squid/vectorops.h
msa/src/ClustalOmega/src/squid/version.h
msa/src/ClustalOmega/src/squid/weight.c
msa/src/ClustalOmega/windows
msa/src/ClustalOmega/windows/src
msa/src/ClustalOmega/windows/src/clustal-omega-config.h
msa/src/ClustalOmega/windows/src/config.h
msa/src/ClustalW
msa/src/ClustalW/COPYING
msa/src/ClustalW/COPYING.LESSER
msa/src/ClustalW/Makefile.am
msa/src/ClustalW/Makefile.in
msa/src/ClustalW/aclocal.m4
msa/src/ClustalW/clustalw_help
msa/src/ClustalW/config.guess
msa/src/ClustalW/config.sub
msa/src/ClustalW/configure
msa/src/ClustalW/configure.ac
msa/src/ClustalW/depcomp
msa/src/ClustalW/install-sh
msa/src/ClustalW/m4
msa/src/ClustalW/m4/Makefile.am
msa/src/ClustalW/m4/Makefile.in
msa/src/ClustalW/missing
msa/src/ClustalW/msaMakefile
msa/src/ClustalW/msaMakefile.win
msa/src/ClustalW/src
msa/src/ClustalW/src/Clustal.cpp
msa/src/ClustalW/src/Clustal.h
msa/src/ClustalW/src/Help.cpp
msa/src/ClustalW/src/Help.h
msa/src/ClustalW/src/Makefile.am
msa/src/ClustalW/src/Makefile.in
msa/src/ClustalW/src/RClustalW.cpp
msa/src/ClustalW/src/RClustalW.h
msa/src/ClustalW/src/RClustalWMain.cpp
msa/src/ClustalW/src/RClustalWMain.h
msa/src/ClustalW/src/alignment
msa/src/ClustalW/src/alignment/Alignment.cpp
msa/src/ClustalW/src/alignment/Alignment.h
msa/src/ClustalW/src/alignment/AlignmentOutput.cpp
msa/src/ClustalW/src/alignment/AlignmentOutput.h
msa/src/ClustalW/src/alignment/ObjectiveScore.cpp
msa/src/ClustalW/src/alignment/ObjectiveScore.h
msa/src/ClustalW/src/alignment/Sequence.cpp
msa/src/ClustalW/src/alignment/Sequence.h
msa/src/ClustalW/src/clustalw_version.h
msa/src/ClustalW/src/clustalw_version.h.in
msa/src/ClustalW/src/config.h.in
msa/src/ClustalW/src/fileInput
msa/src/ClustalW/src/fileInput/ClustalFileParser.cpp
msa/src/ClustalW/src/fileInput/ClustalFileParser.h
msa/src/ClustalW/src/fileInput/EMBLFileParser.cpp
msa/src/ClustalW/src/fileInput/EMBLFileParser.h
msa/src/ClustalW/src/fileInput/FileParser.cpp
msa/src/ClustalW/src/fileInput/FileParser.h
msa/src/ClustalW/src/fileInput/FileReader.cpp
msa/src/ClustalW/src/fileInput/FileReader.h
msa/src/ClustalW/src/fileInput/GDEFileParser.cpp
msa/src/ClustalW/src/fileInput/GDEFileParser.h
msa/src/ClustalW/src/fileInput/InFileStream.cpp
msa/src/ClustalW/src/fileInput/InFileStream.h
msa/src/ClustalW/src/fileInput/MSFFileParser.cpp
msa/src/ClustalW/src/fileInput/MSFFileParser.h
msa/src/ClustalW/src/fileInput/PIRFileParser.cpp
msa/src/ClustalW/src/fileInput/PIRFileParser.h
msa/src/ClustalW/src/fileInput/PearsonFileParser.cpp
msa/src/ClustalW/src/fileInput/PearsonFileParser.h
msa/src/ClustalW/src/fileInput/RSFFileParser.cpp
msa/src/ClustalW/src/fileInput/RSFFileParser.h
msa/src/ClustalW/src/general
msa/src/ClustalW/src/general/Array2D.h
msa/src/ClustalW/src/general/ClustalWResources.cpp
msa/src/ClustalW/src/general/ClustalWResources.h
msa/src/ClustalW/src/general/DebugLog.cpp
msa/src/ClustalW/src/general/DebugLog.h
msa/src/ClustalW/src/general/InvalidCombination.cpp
msa/src/ClustalW/src/general/OutputFile.cpp
msa/src/ClustalW/src/general/OutputFile.h
msa/src/ClustalW/src/general/RandomAccessLList.h
msa/src/ClustalW/src/general/SequenceNotFoundException.h
msa/src/ClustalW/src/general/SquareMat.h
msa/src/ClustalW/src/general/Stats.cpp
msa/src/ClustalW/src/general/Stats.h
msa/src/ClustalW/src/general/SymMatrix.cpp
msa/src/ClustalW/src/general/SymMatrix.h
msa/src/ClustalW/src/general/UserParameters.cpp
msa/src/ClustalW/src/general/UserParameters.h
msa/src/ClustalW/src/general/Utility.cpp
msa/src/ClustalW/src/general/Utility.h
msa/src/ClustalW/src/general/VectorOutOfRange.cpp
msa/src/ClustalW/src/general/VectorOutOfRange.h
msa/src/ClustalW/src/general/VectorUtility.h
msa/src/ClustalW/src/general/clustalw.h
msa/src/ClustalW/src/general/debuglogObject.h
msa/src/ClustalW/src/general/general.h
msa/src/ClustalW/src/general/param.h
msa/src/ClustalW/src/general/statsObject.h
msa/src/ClustalW/src/general/userparams.h
msa/src/ClustalW/src/general/utils.h
msa/src/ClustalW/src/interface
msa/src/ClustalW/src/interface/CommandLineParser.cpp
msa/src/ClustalW/src/interface/CommandLineParser.h
msa/src/ClustalW/src/interface/InteractiveMenu.cpp
msa/src/ClustalW/src/interface/InteractiveMenu.h
msa/src/ClustalW/src/main.cpp
msa/src/ClustalW/src/multipleAlign
msa/src/ClustalW/src/multipleAlign/Iteration.cpp
msa/src/ClustalW/src/multipleAlign/Iteration.h
msa/src/ClustalW/src/multipleAlign/LowScoreSegProfile.cpp
msa/src/ClustalW/src/multipleAlign/LowScoreSegProfile.h
msa/src/ClustalW/src/multipleAlign/MSA.cpp
msa/src/ClustalW/src/multipleAlign/MSA.h
msa/src/ClustalW/src/multipleAlign/MyersMillerProfileAlign.cpp
msa/src/ClustalW/src/multipleAlign/MyersMillerProfileAlign.h
msa/src/ClustalW/src/multipleAlign/ProfileAlignAlgorithm.h
msa/src/ClustalW/src/multipleAlign/ProfileBase.cpp
msa/src/ClustalW/src/multipleAlign/ProfileBase.h
msa/src/ClustalW/src/multipleAlign/ProfileStandard.cpp
msa/src/ClustalW/src/multipleAlign/ProfileStandard.h
msa/src/ClustalW/src/multipleAlign/ProfileWithSub.cpp
msa/src/ClustalW/src/multipleAlign/ProfileWithSub.h
msa/src/ClustalW/src/pairwise
msa/src/ClustalW/src/pairwise/FastPairwiseAlign.cpp
msa/src/ClustalW/src/pairwise/FastPairwiseAlign.h
msa/src/ClustalW/src/pairwise/FullPairwiseAlign.cpp
msa/src/ClustalW/src/pairwise/FullPairwiseAlign.h
msa/src/ClustalW/src/pairwise/PairwiseAlignBase.h
msa/src/ClustalW/src/substitutionMatrix
msa/src/ClustalW/src/substitutionMatrix/SubMatrix.cpp
msa/src/ClustalW/src/substitutionMatrix/SubMatrix.h
msa/src/ClustalW/src/substitutionMatrix/globalmatrix.h
msa/src/ClustalW/src/substitutionMatrix/matrices.h
msa/src/ClustalW/src/tree
msa/src/ClustalW/src/tree/AlignmentSteps.cpp
msa/src/ClustalW/src/tree/AlignmentSteps.h
msa/src/ClustalW/src/tree/ClusterTree.cpp
msa/src/ClustalW/src/tree/ClusterTree.h
msa/src/ClustalW/src/tree/ClusterTreeAlgorithm.h
msa/src/ClustalW/src/tree/ClusterTreeOutput.cpp
msa/src/ClustalW/src/tree/ClusterTreeOutput.h
msa/src/ClustalW/src/tree/NJTree.cpp
msa/src/ClustalW/src/tree/NJTree.h
msa/src/ClustalW/src/tree/RandomGenerator.cpp
msa/src/ClustalW/src/tree/RandomGenerator.h
msa/src/ClustalW/src/tree/Tree.cpp
msa/src/ClustalW/src/tree/Tree.h
msa/src/ClustalW/src/tree/TreeInterface.cpp
msa/src/ClustalW/src/tree/TreeInterface.h
msa/src/ClustalW/src/tree/UPGMA
msa/src/ClustalW/src/tree/UPGMA/Node.cpp
msa/src/ClustalW/src/tree/UPGMA/Node.h
msa/src/ClustalW/src/tree/UPGMA/RootedClusterTree.cpp
msa/src/ClustalW/src/tree/UPGMA/RootedClusterTree.h
msa/src/ClustalW/src/tree/UPGMA/RootedGuideTree.cpp
msa/src/ClustalW/src/tree/UPGMA/RootedGuideTree.h
msa/src/ClustalW/src/tree/UPGMA/RootedTreeOutput.cpp
msa/src/ClustalW/src/tree/UPGMA/RootedTreeOutput.h
msa/src/ClustalW/src/tree/UPGMA/UPGMAAlgorithm.cpp
msa/src/ClustalW/src/tree/UPGMA/UPGMAAlgorithm.h
msa/src/ClustalW/src/tree/UPGMA/upgmadata.h
msa/src/ClustalW/src/tree/UnRootedClusterTree.cpp
msa/src/ClustalW/src/tree/UnRootedClusterTree.h
msa/src/ClustalW/src/tree/dayhoff.h
msa/src/ClustalW/windows
msa/src/ClustalW/windows/Makefile
msa/src/ClustalW/windows/m4
msa/src/ClustalW/windows/m4/Makefile
msa/src/ClustalW/windows/src
msa/src/ClustalW/windows/src/Makefile
msa/src/ClustalW/windows/src/clustalw_version.h
msa/src/ClustalW/windows/src/config.h
msa/src/Makevars
msa/src/Makevars.win
msa/src/Muscle
msa/src/Muscle/Makefile
msa/src/Muscle/README.txt
msa/src/Muscle/RMuscle.cpp
msa/src/Muscle/RMuscle.h
msa/src/Muscle/aligngivenpath.cpp
msa/src/Muscle/aligngivenpathsw.cpp
msa/src/Muscle/aligntwomsas.cpp
msa/src/Muscle/aligntwoprofs.cpp
msa/src/Muscle/aln.cpp
msa/src/Muscle/alpha.cpp
msa/src/Muscle/alpha.h
msa/src/Muscle/anchors.cpp
msa/src/Muscle/bittraceback.cpp
msa/src/Muscle/blosum62.cpp
msa/src/Muscle/blosumla.cpp
msa/src/Muscle/clust.cpp
msa/src/Muscle/clust.h
msa/src/Muscle/cluster.cpp
msa/src/Muscle/cluster.h
msa/src/Muscle/clustset.h
msa/src/Muscle/clustsetdf.h
msa/src/Muscle/clustsetmsa.h
msa/src/Muscle/clwwt.cpp
msa/src/Muscle/color.cpp
msa/src/Muscle/cons.cpp
msa/src/Muscle/diaglist.cpp
msa/src/Muscle/diaglist.h
msa/src/Muscle/diffobjscore.cpp
msa/src/Muscle/diffpaths.cpp
msa/src/Muscle/difftrees.cpp
msa/src/Muscle/difftreese.cpp
msa/src/Muscle/distcalc.cpp
msa/src/Muscle/distcalc.h
msa/src/Muscle/distfunc.cpp
msa/src/Muscle/distfunc.h
msa/src/Muscle/distpwkimura.cpp
msa/src/Muscle/domuscle.cpp
msa/src/Muscle/dosp.cpp
msa/src/Muscle/dpregionlist.h
msa/src/Muscle/dpreglist.cpp
msa/src/Muscle/dpreglist.h
msa/src/Muscle/drawtree.cpp
msa/src/Muscle/edgelist.cpp
msa/src/Muscle/edgelist.h
msa/src/Muscle/enumopts.cpp
msa/src/Muscle/enumopts.h
msa/src/Muscle/enums.h
msa/src/Muscle/enumtostr.cpp
msa/src/Muscle/estring.cpp
msa/src/Muscle/estring.h
msa/src/Muscle/fasta.cpp
msa/src/Muscle/fasta2.cpp
msa/src/Muscle/fastclust.cpp
msa/src/Muscle/fastdist.cpp
msa/src/Muscle/fastdistjones.cpp
msa/src/Muscle/fastdistkbit.cpp
msa/src/Muscle/fastdistkmer.cpp
msa/src/Muscle/fastdistmafft.cpp
msa/src/Muscle/fastdistnuc.cpp
msa/src/Muscle/fastscorepath2.cpp
msa/src/Muscle/finddiags.cpp
msa/src/Muscle/finddiagsn.cpp
msa/src/Muscle/gapscoredimer.h
msa/src/Muscle/gatest.cpp
msa/src/Muscle/glbalign.cpp
msa/src/Muscle/glbalign352.cpp
msa/src/Muscle/glbaligndiag.cpp
msa/src/Muscle/glbalignla.cpp
msa/src/Muscle/glbalignle.cpp
msa/src/Muscle/glbalignns.cpp
msa/src/Muscle/glbalignsimple.cpp
msa/src/Muscle/glbalignsp.cpp
msa/src/Muscle/glbalignspn.cpp
msa/src/Muscle/glbalignss.cpp
msa/src/Muscle/glbalndimer.cpp
msa/src/Muscle/globals.cpp
msa/src/Muscle/globalslinux.cpp
msa/src/Muscle/globalsosx.cpp
msa/src/Muscle/globalsother.cpp
msa/src/Muscle/globalswin32.cpp
msa/src/Muscle/gonnet.cpp
msa/src/Muscle/gonnet.h
msa/src/Muscle/gotowt.cpp
msa/src/Muscle/henikoffweight.cpp
msa/src/Muscle/henikoffweightpb.cpp
msa/src/Muscle/html.cpp
msa/src/Muscle/hydro.cpp
msa/src/Muscle/intmath.cpp
msa/src/Muscle/intmath.h
msa/src/Muscle/local.cpp
msa/src/Muscle/main.cpp
msa/src/Muscle/make.err
msa/src/Muscle/make.out
msa/src/Muscle/makerootmsa.cpp
msa/src/Muscle/makerootmsab.cpp
msa/src/Muscle/maketree.cpp
msa/src/Muscle/mhack.cpp
msa/src/Muscle/mk
msa/src/Muscle/mpam200.cpp
msa/src/Muscle/msa.cpp
msa/src/Muscle/msa.h
msa/src/Muscle/msa2.cpp
msa/src/Muscle/msaMakefile
msa/src/Muscle/msaMakefile.win
msa/src/Muscle/msadist.h
msa/src/Muscle/msadistkimura.cpp
msa/src/Muscle/msadistkimura.h
msa/src/Muscle/msadistmafft.h
msa/src/Muscle/msf.cpp
msa/src/Muscle/muscle.cpp
msa/src/Muscle/muscle.h
msa/src/Muscle/muscleout.cpp
msa/src/Muscle/nucmx.cpp
msa/src/Muscle/nwdasimple.cpp
msa/src/Muscle/nwdasimple2.cpp
msa/src/Muscle/nwdasmall.cpp
msa/src/Muscle/nwrec.cpp
msa/src/Muscle/nwsmall.cpp
msa/src/Muscle/objscore.cpp
msa/src/Muscle/objscore.h
msa/src/Muscle/objscore2.cpp
msa/src/Muscle/objscoreda.cpp
msa/src/Muscle/onexception.cpp
msa/src/Muscle/options.cpp
msa/src/Muscle/outweights.cpp
msa/src/Muscle/pam200mafft.cpp
msa/src/Muscle/params.cpp
msa/src/Muscle/params.h
msa/src/Muscle/phy.cpp
msa/src/Muscle/phy2.cpp
msa/src/Muscle/phy3.cpp
msa/src/Muscle/phy4.cpp
msa/src/Muscle/phyfromclust.cpp
msa/src/Muscle/phyfromfile.cpp
msa/src/Muscle/physeq.cpp
msa/src/Muscle/phytofile.cpp
msa/src/Muscle/posgap.cpp
msa/src/Muscle/ppscore.cpp
msa/src/Muscle/profdb.cpp
msa/src/Muscle/profile.cpp
msa/src/Muscle/profile.h
msa/src/Muscle/profilefrommsa.cpp
msa/src/Muscle/progalign.cpp
msa/src/Muscle/progress.cpp
msa/src/Muscle/progressivealign.cpp
msa/src/Muscle/pwpath.cpp
msa/src/Muscle/pwpath.h
msa/src/Muscle/readmx.cpp
msa/src/Muscle/realigndiffs.cpp
msa/src/Muscle/realigndiffse.cpp
msa/src/Muscle/redblack.cpp
msa/src/Muscle/refine.cpp
msa/src/Muscle/refinehoriz.cpp
msa/src/Muscle/refinesubfams.cpp
msa/src/Muscle/refinetree.cpp
msa/src/Muscle/refinetreee.cpp
msa/src/Muscle/refinevert.cpp
msa/src/Muscle/refinew.cpp
msa/src/Muscle/releases.txt
msa/src/Muscle/savebest.cpp
msa/src/Muscle/scoredist.cpp
msa/src/Muscle/scoregaps.cpp
msa/src/Muscle/scorehistory.cpp
msa/src/Muscle/scorehistory.h
msa/src/Muscle/scoremx.cpp
msa/src/Muscle/scorepp.cpp
msa/src/Muscle/seq.cpp
msa/src/Muscle/seq.h
msa/src/Muscle/seqvect.cpp
msa/src/Muscle/seqvect.h
msa/src/Muscle/setblosumweights.cpp
msa/src/Muscle/setgscweights.cpp
msa/src/Muscle/setnewhandler.cpp
msa/src/Muscle/spfast.cpp
msa/src/Muscle/sptest.cpp
msa/src/Muscle/stabilize.cpp
msa/src/Muscle/subfam.cpp
msa/src/Muscle/subfams.cpp
msa/src/Muscle/svnmods.h
msa/src/Muscle/svnversion.h
msa/src/Muscle/sw.cpp
msa/src/Muscle/termgaps.cpp
msa/src/Muscle/textfile.cpp
msa/src/Muscle/textfile.h
msa/src/Muscle/threewaywt.cpp
msa/src/Muscle/timing.h
msa/src/Muscle/tomhydro.cpp
msa/src/Muscle/traceback.cpp
msa/src/Muscle/tracebackopt.cpp
msa/src/Muscle/tracebacksw.cpp
msa/src/Muscle/tree.h
msa/src/Muscle/treefrommsa.cpp
msa/src/Muscle/types.h
msa/src/Muscle/typetostr.cpp
msa/src/Muscle/unixio.h
msa/src/Muscle/upgma2.cpp
msa/src/Muscle/usage.cpp
msa/src/Muscle/validateids.cpp
msa/src/Muscle/version.txt
msa/src/Muscle/vtml2.cpp
msa/src/Muscle/writescorefile.cpp
msa/src/R_init_msa.cpp
msa/src/SplitCharVector2List.cpp
msa/src/SplitCharVector2List.h
msa/src/SplitCharVector2Matrix.cpp
msa/src/SplitCharVector2Matrix.h
msa/src/gc-7.2
msa/src/gc-7.2/BCC_MAKEFILE
msa/src/gc-7.2/CMakeLists.txt
msa/src/gc-7.2/ChangeLog
msa/src/gc-7.2/EMX_MAKEFILE
msa/src/gc-7.2/MacProjects.sit.hqx
msa/src/gc-7.2/Mac_files
msa/src/gc-7.2/Mac_files/MacOS_Test_config.h
msa/src/gc-7.2/Mac_files/MacOS_config.h
msa/src/gc-7.2/Mac_files/dataend.c
msa/src/gc-7.2/Mac_files/datastart.c
msa/src/gc-7.2/Makefile.DLLs
msa/src/gc-7.2/Makefile.am
msa/src/gc-7.2/Makefile.direct
msa/src/gc-7.2/Makefile.dj
msa/src/gc-7.2/Makefile.in
msa/src/gc-7.2/NT_MAKEFILE
msa/src/gc-7.2/NT_STATIC_THREADS_MAKEFILE
msa/src/gc-7.2/NT_X64_STATIC_THREADS_MAKEFILE
msa/src/gc-7.2/NT_X64_THREADS_MAKEFILE
msa/src/gc-7.2/OS2_MAKEFILE
msa/src/gc-7.2/PCR-Makefile
msa/src/gc-7.2/README.QUICK
msa/src/gc-7.2/SMakefile.amiga
msa/src/gc-7.2/WCC_MAKEFILE
msa/src/gc-7.2/aclocal.m4
msa/src/gc-7.2/allchblk.c
msa/src/gc-7.2/alloc.c
msa/src/gc-7.2/alpha_mach_dep.S
msa/src/gc-7.2/autogen.sh
msa/src/gc-7.2/backgraph.c
msa/src/gc-7.2/bdw-gc.pc.in
msa/src/gc-7.2/blacklst.c
msa/src/gc-7.2/build_atomic_ops.sh
msa/src/gc-7.2/build_atomic_ops.sh.cygwin
msa/src/gc-7.2/callprocs
msa/src/gc-7.2/checksums.c
msa/src/gc-7.2/compile
msa/src/gc-7.2/config.guess
msa/src/gc-7.2/config.sub
msa/src/gc-7.2/configure
msa/src/gc-7.2/configure.ac
msa/src/gc-7.2/configure.host
msa/src/gc-7.2/cord
msa/src/gc-7.2/cord/cord.am
msa/src/gc-7.2/cord/cordbscs.c
msa/src/gc-7.2/cord/cordprnt.c
msa/src/gc-7.2/cord/cordtest.c
msa/src/gc-7.2/cord/cordxtra.c
msa/src/gc-7.2/cord/de.c
msa/src/gc-7.2/cord/de_cmds.h
msa/src/gc-7.2/cord/de_win.ICO
msa/src/gc-7.2/cord/de_win.RC
msa/src/gc-7.2/cord/de_win.c
msa/src/gc-7.2/cord/de_win.h
msa/src/gc-7.2/darwin_stop_world.c
msa/src/gc-7.2/dbg_mlc.c
msa/src/gc-7.2/depcomp
msa/src/gc-7.2/digimars.mak
msa/src/gc-7.2/doc
msa/src/gc-7.2/doc/README
msa/src/gc-7.2/doc/README.DGUX386
msa/src/gc-7.2/doc/README.Mac
msa/src/gc-7.2/doc/README.MacOSX
msa/src/gc-7.2/doc/README.OS2
msa/src/gc-7.2/doc/README.amiga
msa/src/gc-7.2/doc/README.arm.cross
msa/src/gc-7.2/doc/README.autoconf
msa/src/gc-7.2/doc/README.changes
msa/src/gc-7.2/doc/README.cmake
msa/src/gc-7.2/doc/README.contributors
msa/src/gc-7.2/doc/README.cords
msa/src/gc-7.2/doc/README.darwin
msa/src/gc-7.2/doc/README.dj
msa/src/gc-7.2/doc/README.environment
msa/src/gc-7.2/doc/README.ews4800
msa/src/gc-7.2/doc/README.hp
msa/src/gc-7.2/doc/README.linux
msa/src/gc-7.2/doc/README.macros
msa/src/gc-7.2/doc/README.rs6000
msa/src/gc-7.2/doc/README.sgi
msa/src/gc-7.2/doc/README.solaris2
msa/src/gc-7.2/doc/README.uts
msa/src/gc-7.2/doc/README.win32
msa/src/gc-7.2/doc/README.win64
msa/src/gc-7.2/doc/barrett_diagram
msa/src/gc-7.2/doc/debugging.html
msa/src/gc-7.2/doc/doc.am
msa/src/gc-7.2/doc/gc.man
msa/src/gc-7.2/doc/gcdescr.html
msa/src/gc-7.2/doc/gcinterface.html
msa/src/gc-7.2/doc/leak.html
msa/src/gc-7.2/doc/overview.html
msa/src/gc-7.2/doc/porting.html
msa/src/gc-7.2/doc/scale.html
msa/src/gc-7.2/doc/simple_example.html
msa/src/gc-7.2/doc/tree.html
msa/src/gc-7.2/dyn_load.c
msa/src/gc-7.2/extra
msa/src/gc-7.2/extra/AmigaOS.c
msa/src/gc-7.2/extra/MacOS.c
msa/src/gc-7.2/extra/add_gc_prefix.c
msa/src/gc-7.2/extra/gc.c
msa/src/gc-7.2/extra/gcname.c
msa/src/gc-7.2/extra/if_mach.c
msa/src/gc-7.2/extra/if_not_there.c
msa/src/gc-7.2/extra/msvc_dbg.c
msa/src/gc-7.2/extra/setjmp_t.c
msa/src/gc-7.2/extra/threadlibs.c
msa/src/gc-7.2/finalize.c
msa/src/gc-7.2/gc.mak
msa/src/gc-7.2/gc_cpp.cc
msa/src/gc-7.2/gc_cpp.cpp
msa/src/gc-7.2/gc_dlopen.c
msa/src/gc-7.2/gcj_mlc.c
msa/src/gc-7.2/headers.c
msa/src/gc-7.2/ia64_save_regs_in_stack.s
msa/src/gc-7.2/include
msa/src/gc-7.2/include/cord.h
msa/src/gc-7.2/include/ec.h
msa/src/gc-7.2/include/extra
msa/src/gc-7.2/include/extra/gc.h
msa/src/gc-7.2/include/extra/gc_cpp.h
msa/src/gc-7.2/include/gc.h
msa/src/gc-7.2/include/gc_allocator.h
msa/src/gc-7.2/include/gc_amiga_redirects.h
msa/src/gc-7.2/include/gc_backptr.h
msa/src/gc-7.2/include/gc_config_macros.h
msa/src/gc-7.2/include/gc_cpp.h
msa/src/gc-7.2/include/gc_gcj.h
msa/src/gc-7.2/include/gc_inline.h
msa/src/gc-7.2/include/gc_mark.h
msa/src/gc-7.2/include/gc_pthread_redirects.h
msa/src/gc-7.2/include/gc_tiny_fl.h
msa/src/gc-7.2/include/gc_typed.h
msa/src/gc-7.2/include/gc_version.h
msa/src/gc-7.2/include/include.am
msa/src/gc-7.2/include/javaxfc.h
msa/src/gc-7.2/include/leak_detector.h
msa/src/gc-7.2/include/new_gc_alloc.h
msa/src/gc-7.2/include/private
msa/src/gc-7.2/include/private/config.h.in
msa/src/gc-7.2/include/private/cord_pos.h
msa/src/gc-7.2/include/private/darwin_semaphore.h
msa/src/gc-7.2/include/private/darwin_stop_world.h
msa/src/gc-7.2/include/private/dbg_mlc.h
msa/src/gc-7.2/include/private/gc_hdrs.h
msa/src/gc-7.2/include/private/gc_locks.h
msa/src/gc-7.2/include/private/gc_pmark.h
msa/src/gc-7.2/include/private/gc_priv.h
msa/src/gc-7.2/include/private/gcconfig.h
msa/src/gc-7.2/include/private/msvc_dbg.h
msa/src/gc-7.2/include/private/pthread_stop_world.h
msa/src/gc-7.2/include/private/pthread_support.h
msa/src/gc-7.2/include/private/specific.h
msa/src/gc-7.2/include/private/thread_local_alloc.h
msa/src/gc-7.2/include/weakpointer.h
msa/src/gc-7.2/install-sh
msa/src/gc-7.2/libatomic_ops
msa/src/gc-7.2/libatomic_ops/AUTHORS
msa/src/gc-7.2/libatomic_ops/COPYING
msa/src/gc-7.2/libatomic_ops/ChangeLog
msa/src/gc-7.2/libatomic_ops/INSTALL
msa/src/gc-7.2/libatomic_ops/Makefile.am
msa/src/gc-7.2/libatomic_ops/Makefile.in
msa/src/gc-7.2/libatomic_ops/NEWS
msa/src/gc-7.2/libatomic_ops/README
msa/src/gc-7.2/libatomic_ops/aclocal.m4
msa/src/gc-7.2/libatomic_ops/compile
msa/src/gc-7.2/libatomic_ops/config.guess
msa/src/gc-7.2/libatomic_ops/config.sub
msa/src/gc-7.2/libatomic_ops/configure
msa/src/gc-7.2/libatomic_ops/configure.ac
msa/src/gc-7.2/libatomic_ops/depcomp
msa/src/gc-7.2/libatomic_ops/doc
msa/src/gc-7.2/libatomic_ops/doc/COPYING
msa/src/gc-7.2/libatomic_ops/doc/LICENSING.txt
msa/src/gc-7.2/libatomic_ops/doc/Makefile.am
msa/src/gc-7.2/libatomic_ops/doc/Makefile.in
msa/src/gc-7.2/libatomic_ops/doc/README.txt
msa/src/gc-7.2/libatomic_ops/doc/README_malloc.txt
msa/src/gc-7.2/libatomic_ops/doc/README_stack.txt
msa/src/gc-7.2/libatomic_ops/doc/README_win32.txt
msa/src/gc-7.2/libatomic_ops/install-sh
msa/src/gc-7.2/libatomic_ops/missing
msa/src/gc-7.2/libatomic_ops/mkinstalldirs
msa/src/gc-7.2/libatomic_ops/pkgconfig
msa/src/gc-7.2/libatomic_ops/pkgconfig/atomic_ops-uninstalled.pc.in
msa/src/gc-7.2/libatomic_ops/pkgconfig/atomic_ops.pc.in
msa/src/gc-7.2/libatomic_ops/src
msa/src/gc-7.2/libatomic_ops/src/Makefile.am
msa/src/gc-7.2/libatomic_ops/src/Makefile.in
msa/src/gc-7.2/libatomic_ops/src/Makefile.msft
msa/src/gc-7.2/libatomic_ops/src/atomic_ops
msa/src/gc-7.2/libatomic_ops/src/atomic_ops.c
msa/src/gc-7.2/libatomic_ops/src/atomic_ops.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/Makefile.am
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/Makefile.in
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/generalize-small.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/generalize-small.template
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/generalize.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/Makefile.am
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/Makefile.in
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/README
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/acquire_release_volatile.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/aligned_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/all_acquire_release_volatile.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/all_aligned_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/all_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/ao_t_is_int.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/armcc
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/armcc/arm_v6.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/char_acquire_release_volatile.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/char_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/emul_cas.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/alpha.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/arm.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/avr32.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/cris.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/hexagon.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/hppa.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/ia64.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/m68k.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/mips.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/powerpc.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/s390.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/sh.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/sparc.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/x86.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/gcc/x86_64.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/generic_pthread.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/hpc
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/hpc/hppa.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/hpc/ia64.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/ibmc
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/ibmc/powerpc.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/icc
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/icc/ia64.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/int_acquire_release_volatile.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/int_aligned_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/int_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/msftc
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/msftc/arm.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/msftc/common32_defs.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/msftc/x86.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/msftc/x86_64.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/ordered.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/ordered_except_wr.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/read_ordered.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/short_acquire_release_volatile.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/short_aligned_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/short_atomic_load_store.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/standard_ao_double_t.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/sunc
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/sunc/sparc.S
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/sunc/sparc.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/sunc/x86.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/sunc/x86_64.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/test_and_set_t_is_ao_t.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops/sysdeps/test_and_set_t_is_char.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops_malloc.c
msa/src/gc-7.2/libatomic_ops/src/atomic_ops_malloc.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops_stack.c
msa/src/gc-7.2/libatomic_ops/src/atomic_ops_stack.h
msa/src/gc-7.2/libatomic_ops/src/atomic_ops_sysdeps.S
msa/src/gc-7.2/libatomic_ops/src/config.h.in
msa/src/gc-7.2/libatomic_ops/test-driver
msa/src/gc-7.2/libatomic_ops/tests
msa/src/gc-7.2/libatomic_ops/tests/Makefile.am
msa/src/gc-7.2/libatomic_ops/tests/Makefile.in
msa/src/gc-7.2/libatomic_ops/tests/list_atomic.c
msa/src/gc-7.2/libatomic_ops/tests/list_atomic.template
msa/src/gc-7.2/libatomic_ops/tests/run_parallel.inc
msa/src/gc-7.2/libatomic_ops/tests/test_atomic.c
msa/src/gc-7.2/libatomic_ops/tests/test_atomic.template
msa/src/gc-7.2/libatomic_ops/tests/test_atomic_include.h
msa/src/gc-7.2/libatomic_ops/tests/test_malloc.c
msa/src/gc-7.2/libatomic_ops/tests/test_stack.c
msa/src/gc-7.2/ltmain.sh
msa/src/gc-7.2/m4
msa/src/gc-7.2/m4/gc_set_version.m4
msa/src/gc-7.2/m4/libtool.m4
msa/src/gc-7.2/m4/ltoptions.m4
msa/src/gc-7.2/m4/ltsugar.m4
msa/src/gc-7.2/m4/ltversion.m4
msa/src/gc-7.2/mach_dep.c
msa/src/gc-7.2/malloc.c
msa/src/gc-7.2/mallocx.c
msa/src/gc-7.2/mark.c
msa/src/gc-7.2/mark_rts.c
msa/src/gc-7.2/mips_sgi_mach_dep.s
msa/src/gc-7.2/mips_ultrix_mach_dep.s
msa/src/gc-7.2/misc.c
msa/src/gc-7.2/missing
msa/src/gc-7.2/mkinstalldirs
msa/src/gc-7.2/msaMakefile
msa/src/gc-7.2/msaMakefile.win
msa/src/gc-7.2/new_hblk.c
msa/src/gc-7.2/obj_map.c
msa/src/gc-7.2/os_dep.c
msa/src/gc-7.2/pcr_interface.c
msa/src/gc-7.2/pthread_start.c
msa/src/gc-7.2/pthread_stop_world.c
msa/src/gc-7.2/pthread_support.c
msa/src/gc-7.2/ptr_chck.c
msa/src/gc-7.2/real_malloc.c
msa/src/gc-7.2/reclaim.c
msa/src/gc-7.2/rs6000_mach_dep.s
msa/src/gc-7.2/sparc_mach_dep.S
msa/src/gc-7.2/sparc_netbsd_mach_dep.s
msa/src/gc-7.2/sparc_sunos4_mach_dep.s
msa/src/gc-7.2/specific.c
msa/src/gc-7.2/stubborn.c
msa/src/gc-7.2/test-driver
msa/src/gc-7.2/tests
msa/src/gc-7.2/tests/CMakeLists.txt
msa/src/gc-7.2/tests/huge_test.c
msa/src/gc-7.2/tests/initsecondarythread.c
msa/src/gc-7.2/tests/leak_test.c
msa/src/gc-7.2/tests/middle.c
msa/src/gc-7.2/tests/realloc_test.c
msa/src/gc-7.2/tests/smash_test.c
msa/src/gc-7.2/tests/staticrootslib.c
msa/src/gc-7.2/tests/staticrootstest.c
msa/src/gc-7.2/tests/test.c
msa/src/gc-7.2/tests/test_cpp.cc
msa/src/gc-7.2/tests/tests.am
msa/src/gc-7.2/tests/thread_leak_test.c
msa/src/gc-7.2/tests/threadkey_test.c
msa/src/gc-7.2/tests/trace_test.c
msa/src/gc-7.2/thread_local_alloc.c
msa/src/gc-7.2/typd_mlc.c
msa/src/gc-7.2/win32_threads.c
msa/vignettes
msa/vignettes/JKU_EN_noName.pdf
msa/vignettes/SweaveExample.txt
msa/vignettes/bioinf-article.txi
msa/vignettes/bioinf-bar.png
msa/vignettes/bioinf.cls
msa/vignettes/knitrExample.txt
msa/vignettes/lit.bib
msa/vignettes/msa.Rnw
msa/vignettes/texshade.sty

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.