msa: Multiple Sequence Alignment
Version 1.8.0

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
Bioconductor views Alignment MultipleComparison MultipleSequenceAlignment Sequencing
Date of publicationNone
MaintainerUlrich Bodenhofer <bodenhofer@bioinf.jku.at>
LicenseGPL (>= 2)
Version1.8.0
URL http://www.bioinf.jku.at/software/msa/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("msa")

Getting started

Package overview

Popular man pages

msaCheckNames: Check and fix sequence names
msaClustalW: Multiple Sequence Alignment with ClustalW
msaConsensusSequence-methods: Computation of Consensus Sequence from Multiple Alignment
msaConvert: Convert Multiple Sequence Alignment for Other Packages
MsaMetaData-class: Class 'MsaMetaData'
MsaMultipleAlignmentClasses: Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment',...
msaPrettyPrint: Pretty-Printing of Multiple Sequence Alignments
See all...

All man pages Function index File listing

Man pages

msa: Unified interface to multiple sequence alignment algorithms
msaCheckNames: Check and fix sequence names
msaClustalOmega: Multiple Sequence Alignment with ClustalOmega
msaClustalW: Multiple Sequence Alignment with ClustalW
msaConsensusSequence-methods: Computation of Consensus Sequence from Multiple Alignment
msaConservationScore-methods: Computation of Conservation Scores from Multiple Alignment
msaConvert: Convert Multiple Sequence Alignment for Other Packages
MsaMetaData-class: Class 'MsaMetaData'
MsaMultipleAlignmentClasses: Classes 'MsaAAMultipleAlignment', 'MsaDNAMultipleAlignment',...
msaMuscle: Multiple Sequence Alignment with MUSCLE
msa-package: Multiple Sequence Alignment
msaPrettyPrint: Pretty-Printing of Multiple Sequence Alignments

Functions

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/convertRows.R
R/helperFunctions.R
R/inputChecks.R
R/msa.R
R/msaCheckNames.R
R/msaClustalOmega.R
R/msaClustalW.R
R/msaConsensusSequence-methods.R
R/msaConservationScore-methods.R
R/msaConvert.R
R/msaMuscle.R
R/msaPrettyPrint.R
R/params-methods.R
R/print-methods.R
R/show-methods.R
R/version-methods.R
build
build/vignette.rds
cleanup
cleanup.win
inst
inst/CITATION
inst/COPYRIGHT
inst/NEWS
inst/doc
inst/doc/msa.R
inst/doc/msa.Rnw
inst/doc/msa.pdf
inst/examples
inst/examples/HemoglobinAA.fasta
inst/examples/exampleAA.fasta
inst/examples/exampleDNA.fasta
inst/examples/exampleRNA.fasta
inst/extdata
inst/extdata/msaClustalOmegaHelp.txt
inst/extdata/msaClustalWHelp.txt
inst/extdata/msaCommonHelp.txt
inst/extdata/msaHelpPrefix.txt
inst/extdata/msaMuscleHelp.txt
inst/tex
inst/tex/texshade.sty
man
man/MsaMetaData-class.Rd
man/MsaMultipleAlignmentClasses.Rd
man/msa-package.Rd
man/msa.Rd
man/msaCheckNames.Rd
man/msaClustalOmega.Rd
man/msaClustalW.Rd
man/msaConsensusSequence-methods.Rd
man/msaConservationScore-methods.Rd
man/msaConvert.Rd
man/msaMuscle.Rd
man/msaPrettyPrint.Rd
src
src/ClustalOmega
src/ClustalOmega/AUTHORS
src/ClustalOmega/COPYING
src/ClustalOmega/Doxyfile
src/ClustalOmega/Doxyfile.in
src/ClustalOmega/Makefile.am
src/ClustalOmega/Makefile.in
src/ClustalOmega/aclocal.m4
src/ClustalOmega/clustalo.pc.in
src/ClustalOmega/config.guess
src/ClustalOmega/config.sub
src/ClustalOmega/configure
src/ClustalOmega/configure.ac
src/ClustalOmega/depcomp
src/ClustalOmega/install-sh
src/ClustalOmega/ltmain.sh
src/ClustalOmega/m4
src/ClustalOmega/m4/ax_openmp.m4
src/ClustalOmega/m4/ax_prefix_config_h.m4
src/ClustalOmega/m4/libtool.m4
src/ClustalOmega/m4/ltoptions.m4
src/ClustalOmega/m4/ltsugar.m4
src/ClustalOmega/m4/ltversion.m4
src/ClustalOmega/missing
src/ClustalOmega/msaMakefile
src/ClustalOmega/msaMakefile.win
src/ClustalOmega/src
src/ClustalOmega/src/Makefile.am
src/ClustalOmega/src/Makefile.in
src/ClustalOmega/src/RClustalOmega.cpp
src/ClustalOmega/src/RClustalOmega.h
src/ClustalOmega/src/argtable2
src/ClustalOmega/src/argtable2/CMakeLists.txt
src/ClustalOmega/src/argtable2/Makefile.am
src/ClustalOmega/src/argtable2/Makefile.in
src/ClustalOmega/src/argtable2/Makefile.nmake
src/ClustalOmega/src/argtable2/arg_date.c
src/ClustalOmega/src/argtable2/arg_dbl.c
src/ClustalOmega/src/argtable2/arg_end.c
src/ClustalOmega/src/argtable2/arg_file.c
src/ClustalOmega/src/argtable2/arg_int.c
src/ClustalOmega/src/argtable2/arg_lit.c
src/ClustalOmega/src/argtable2/arg_rem.c
src/ClustalOmega/src/argtable2/arg_rex.c
src/ClustalOmega/src/argtable2/arg_str.c
src/ClustalOmega/src/argtable2/argtable2.c
src/ClustalOmega/src/argtable2/argtable2.def
src/ClustalOmega/src/argtable2/argtable2.h
src/ClustalOmega/src/argtable2/config.h
src/ClustalOmega/src/argtable2/config.h.in
src/ClustalOmega/src/argtable2/getopt.c
src/ClustalOmega/src/argtable2/getopt.h
src/ClustalOmega/src/argtable2/getopt1.c
src/ClustalOmega/src/clustal
src/ClustalOmega/src/clustal-omega-config.h
src/ClustalOmega/src/clustal-omega.c
src/ClustalOmega/src/clustal-omega.h
src/ClustalOmega/src/clustal/Makefile.am
src/ClustalOmega/src/clustal/Makefile.in
src/ClustalOmega/src/clustal/hhalign_wrapper.c
src/ClustalOmega/src/clustal/hhalign_wrapper.h
src/ClustalOmega/src/clustal/ktuple_pair.c
src/ClustalOmega/src/clustal/ktuple_pair.h
src/ClustalOmega/src/clustal/list.c
src/ClustalOmega/src/clustal/list.h
src/ClustalOmega/src/clustal/log.c
src/ClustalOmega/src/clustal/log.h
src/ClustalOmega/src/clustal/mbed.c
src/ClustalOmega/src/clustal/mbed.h
src/ClustalOmega/src/clustal/muscle_tree.c
src/ClustalOmega/src/clustal/muscle_tree.h
src/ClustalOmega/src/clustal/muscle_upgma.c
src/ClustalOmega/src/clustal/muscle_upgma.h
src/ClustalOmega/src/clustal/pair_dist.c
src/ClustalOmega/src/clustal/pair_dist.h
src/ClustalOmega/src/clustal/progress.c
src/ClustalOmega/src/clustal/progress.h
src/ClustalOmega/src/clustal/queue.h
src/ClustalOmega/src/clustal/seq.c
src/ClustalOmega/src/clustal/seq.h
src/ClustalOmega/src/clustal/symmatrix.c
src/ClustalOmega/src/clustal/symmatrix.h
src/ClustalOmega/src/clustal/tree.c
src/ClustalOmega/src/clustal/tree.h
src/ClustalOmega/src/clustal/util.c
src/ClustalOmega/src/clustal/util.h
src/ClustalOmega/src/clustal/weights.c
src/ClustalOmega/src/clustal/weights.h
src/ClustalOmega/src/clustalo-api-test.c
src/ClustalOmega/src/config.h.in
src/ClustalOmega/src/exceptions4c
src/ClustalOmega/src/exceptions4c/Makefile.am
src/ClustalOmega/src/exceptions4c/Makefile.in
src/ClustalOmega/src/exceptions4c/config.h
src/ClustalOmega/src/exceptions4c/config.h.in
src/ClustalOmega/src/exceptions4c/e4c_lite.c
src/ClustalOmega/src/exceptions4c/e4c_lite.h
src/ClustalOmega/src/hhalign
src/ClustalOmega/src/hhalign/Makefile.am
src/ClustalOmega/src/hhalign/Makefile.in
src/ClustalOmega/src/hhalign/general.h
src/ClustalOmega/src/hhalign/hash-C.h
src/ClustalOmega/src/hhalign/hash.h
src/ClustalOmega/src/hhalign/hhalign.cpp
src/ClustalOmega/src/hhalign/hhalign.h
src/ClustalOmega/src/hhalign/hhalignment-C.h
src/ClustalOmega/src/hhalign/hhalignment.h
src/ClustalOmega/src/hhalign/hhdecl-C.h
src/ClustalOmega/src/hhalign/hhfullalignment-C.h
src/ClustalOmega/src/hhalign/hhfullalignment.h
src/ClustalOmega/src/hhalign/hhfunc-C.h
src/ClustalOmega/src/hhalign/hhfunc.h
src/ClustalOmega/src/hhalign/hhhalfalignment-C.h
src/ClustalOmega/src/hhalign/hhhalfalignment.h
src/ClustalOmega/src/hhalign/hhhit-C.h
src/ClustalOmega/src/hhalign/hhhit.h
src/ClustalOmega/src/hhalign/hhhitlist-C.h
src/ClustalOmega/src/hhalign/hhhitlist.h
src/ClustalOmega/src/hhalign/hhhmm-C.h
src/ClustalOmega/src/hhalign/hhhmm.h
src/ClustalOmega/src/hhalign/hhmatrices-C.h
src/ClustalOmega/src/hhalign/hhutil-C.h
src/ClustalOmega/src/hhalign/list-C.h
src/ClustalOmega/src/hhalign/list.h
src/ClustalOmega/src/hhalign/util-C.h
src/ClustalOmega/src/kmpp
src/ClustalOmega/src/kmpp/KMeans.cpp
src/ClustalOmega/src/kmpp/KMeans.h
src/ClustalOmega/src/kmpp/KmTree.cpp
src/ClustalOmega/src/kmpp/KmTree.h
src/ClustalOmega/src/kmpp/KmUtils.cpp
src/ClustalOmega/src/kmpp/KmUtils.h
src/ClustalOmega/src/kmpp/Makefile.am
src/ClustalOmega/src/kmpp/Makefile.in
src/ClustalOmega/src/main.cpp
src/ClustalOmega/src/mymain.c
src/ClustalOmega/src/mymain.h
src/ClustalOmega/src/squid
src/ClustalOmega/src/squid/00README
src/ClustalOmega/src/squid/COPYRIGHT
src/ClustalOmega/src/squid/LICENSE
src/ClustalOmega/src/squid/Makefile.am
src/ClustalOmega/src/squid/Makefile.in
src/ClustalOmega/src/squid/a2m.c
src/ClustalOmega/src/squid/aligneval.c
src/ClustalOmega/src/squid/alignio.c
src/ClustalOmega/src/squid/clustal.c
src/ClustalOmega/src/squid/clustalo.README
src/ClustalOmega/src/squid/cluster.c
src/ClustalOmega/src/squid/dayhoff.c
src/ClustalOmega/src/squid/eps.c
src/ClustalOmega/src/squid/file.c
src/ClustalOmega/src/squid/getopt.c
src/ClustalOmega/src/squid/gki.c
src/ClustalOmega/src/squid/gki.h
src/ClustalOmega/src/squid/gsi.c
src/ClustalOmega/src/squid/gsi.h
src/ClustalOmega/src/squid/gsi64.c
src/ClustalOmega/src/squid/gsi64.h
src/ClustalOmega/src/squid/hsregex.c
src/ClustalOmega/src/squid/iupac.c
src/ClustalOmega/src/squid/msa.c
src/ClustalOmega/src/squid/msa.h
src/ClustalOmega/src/squid/msf.c
src/ClustalOmega/src/squid/phylip.c
src/ClustalOmega/src/squid/revcomp.c
src/ClustalOmega/src/squid/rk.c
src/ClustalOmega/src/squid/rk.h
src/ClustalOmega/src/squid/selex.c
src/ClustalOmega/src/squid/seqencode.c
src/ClustalOmega/src/squid/shuffle.c
src/ClustalOmega/src/squid/sqerror.c
src/ClustalOmega/src/squid/sqfuncs.h
src/ClustalOmega/src/squid/sqio.c
src/ClustalOmega/src/squid/squid-1.9g.tar.gz
src/ClustalOmega/src/squid/squid.h
src/ClustalOmega/src/squid/squidcore.c
src/ClustalOmega/src/squid/sre_ctype.c
src/ClustalOmega/src/squid/sre_math.c
src/ClustalOmega/src/squid/sre_random.c
src/ClustalOmega/src/squid/sre_random.h
src/ClustalOmega/src/squid/sre_string.c
src/ClustalOmega/src/squid/ssi.c
src/ClustalOmega/src/squid/ssi.h
src/ClustalOmega/src/squid/stack.c
src/ClustalOmega/src/squid/stockholm.c
src/ClustalOmega/src/squid/stockholm.h
src/ClustalOmega/src/squid/stopwatch.c
src/ClustalOmega/src/squid/stopwatch.h
src/ClustalOmega/src/squid/translate.c
src/ClustalOmega/src/squid/types.c
src/ClustalOmega/src/squid/vectorops.c
src/ClustalOmega/src/squid/vectorops.h
src/ClustalOmega/src/squid/version.h
src/ClustalOmega/src/squid/weight.c
src/ClustalOmega/windows
src/ClustalOmega/windows/src
src/ClustalOmega/windows/src/clustal-omega-config.h
src/ClustalOmega/windows/src/config.h
src/ClustalW
src/ClustalW/COPYING
src/ClustalW/COPYING.LESSER
src/ClustalW/Makefile.am
src/ClustalW/Makefile.in
src/ClustalW/aclocal.m4
src/ClustalW/clustalw_help
src/ClustalW/config.guess
src/ClustalW/config.sub
src/ClustalW/configure
src/ClustalW/configure.ac
src/ClustalW/depcomp
src/ClustalW/install-sh
src/ClustalW/m4
src/ClustalW/m4/Makefile.am
src/ClustalW/m4/Makefile.in
src/ClustalW/missing
src/ClustalW/msaMakefile
src/ClustalW/msaMakefile.win
src/ClustalW/src
src/ClustalW/src/Clustal.cpp
src/ClustalW/src/Clustal.h
src/ClustalW/src/Help.cpp
src/ClustalW/src/Help.h
src/ClustalW/src/Makefile.am
src/ClustalW/src/Makefile.in
src/ClustalW/src/RClustalW.cpp
src/ClustalW/src/RClustalW.h
src/ClustalW/src/RClustalWMain.cpp
src/ClustalW/src/RClustalWMain.h
src/ClustalW/src/alignment
src/ClustalW/src/alignment/Alignment.cpp
src/ClustalW/src/alignment/Alignment.h
src/ClustalW/src/alignment/AlignmentOutput.cpp
src/ClustalW/src/alignment/AlignmentOutput.h
src/ClustalW/src/alignment/ObjectiveScore.cpp
src/ClustalW/src/alignment/ObjectiveScore.h
src/ClustalW/src/alignment/Sequence.cpp
src/ClustalW/src/alignment/Sequence.h
src/ClustalW/src/clustalw_version.h
src/ClustalW/src/clustalw_version.h.in
src/ClustalW/src/config.h.in
src/ClustalW/src/fileInput
src/ClustalW/src/fileInput/ClustalFileParser.cpp
src/ClustalW/src/fileInput/ClustalFileParser.h
src/ClustalW/src/fileInput/EMBLFileParser.cpp
src/ClustalW/src/fileInput/EMBLFileParser.h
src/ClustalW/src/fileInput/FileParser.cpp
src/ClustalW/src/fileInput/FileParser.h
src/ClustalW/src/fileInput/FileReader.cpp
src/ClustalW/src/fileInput/FileReader.h
src/ClustalW/src/fileInput/GDEFileParser.cpp
src/ClustalW/src/fileInput/GDEFileParser.h
src/ClustalW/src/fileInput/InFileStream.cpp
src/ClustalW/src/fileInput/InFileStream.h
src/ClustalW/src/fileInput/MSFFileParser.cpp
src/ClustalW/src/fileInput/MSFFileParser.h
src/ClustalW/src/fileInput/PIRFileParser.cpp
src/ClustalW/src/fileInput/PIRFileParser.h
src/ClustalW/src/fileInput/PearsonFileParser.cpp
src/ClustalW/src/fileInput/PearsonFileParser.h
src/ClustalW/src/fileInput/RSFFileParser.cpp
src/ClustalW/src/fileInput/RSFFileParser.h
src/ClustalW/src/general
src/ClustalW/src/general/Array2D.h
src/ClustalW/src/general/ClustalWResources.cpp
src/ClustalW/src/general/ClustalWResources.h
src/ClustalW/src/general/DebugLog.cpp
src/ClustalW/src/general/DebugLog.h
src/ClustalW/src/general/InvalidCombination.cpp
src/ClustalW/src/general/OutputFile.cpp
src/ClustalW/src/general/OutputFile.h
src/ClustalW/src/general/RandomAccessLList.h
src/ClustalW/src/general/SequenceNotFoundException.h
src/ClustalW/src/general/SquareMat.h
src/ClustalW/src/general/Stats.cpp
src/ClustalW/src/general/Stats.h
src/ClustalW/src/general/SymMatrix.cpp
src/ClustalW/src/general/SymMatrix.h
src/ClustalW/src/general/UserParameters.cpp
src/ClustalW/src/general/UserParameters.h
src/ClustalW/src/general/Utility.cpp
src/ClustalW/src/general/Utility.h
src/ClustalW/src/general/VectorOutOfRange.cpp
src/ClustalW/src/general/VectorOutOfRange.h
src/ClustalW/src/general/VectorUtility.h
src/ClustalW/src/general/clustalw.h
src/ClustalW/src/general/debuglogObject.h
src/ClustalW/src/general/general.h
src/ClustalW/src/general/param.h
src/ClustalW/src/general/statsObject.h
src/ClustalW/src/general/userparams.h
src/ClustalW/src/general/utils.h
src/ClustalW/src/interface
src/ClustalW/src/interface/CommandLineParser.cpp
src/ClustalW/src/interface/CommandLineParser.h
src/ClustalW/src/interface/InteractiveMenu.cpp
src/ClustalW/src/interface/InteractiveMenu.h
src/ClustalW/src/main.cpp
src/ClustalW/src/multipleAlign
src/ClustalW/src/multipleAlign/Iteration.cpp
src/ClustalW/src/multipleAlign/Iteration.h
src/ClustalW/src/multipleAlign/LowScoreSegProfile.cpp
src/ClustalW/src/multipleAlign/LowScoreSegProfile.h
src/ClustalW/src/multipleAlign/MSA.cpp
src/ClustalW/src/multipleAlign/MSA.h
src/ClustalW/src/multipleAlign/MyersMillerProfileAlign.cpp
src/ClustalW/src/multipleAlign/MyersMillerProfileAlign.h
src/ClustalW/src/multipleAlign/ProfileAlignAlgorithm.h
src/ClustalW/src/multipleAlign/ProfileBase.cpp
src/ClustalW/src/multipleAlign/ProfileBase.h
src/ClustalW/src/multipleAlign/ProfileStandard.cpp
src/ClustalW/src/multipleAlign/ProfileStandard.h
src/ClustalW/src/multipleAlign/ProfileWithSub.cpp
src/ClustalW/src/multipleAlign/ProfileWithSub.h
src/ClustalW/src/pairwise
src/ClustalW/src/pairwise/FastPairwiseAlign.cpp
src/ClustalW/src/pairwise/FastPairwiseAlign.h
src/ClustalW/src/pairwise/FullPairwiseAlign.cpp
src/ClustalW/src/pairwise/FullPairwiseAlign.h
src/ClustalW/src/pairwise/PairwiseAlignBase.h
src/ClustalW/src/substitutionMatrix
src/ClustalW/src/substitutionMatrix/SubMatrix.cpp
src/ClustalW/src/substitutionMatrix/SubMatrix.h
src/ClustalW/src/substitutionMatrix/globalmatrix.h
src/ClustalW/src/substitutionMatrix/matrices.h
src/ClustalW/src/tree
src/ClustalW/src/tree/AlignmentSteps.cpp
src/ClustalW/src/tree/AlignmentSteps.h
src/ClustalW/src/tree/ClusterTree.cpp
src/ClustalW/src/tree/ClusterTree.h
src/ClustalW/src/tree/ClusterTreeAlgorithm.h
src/ClustalW/src/tree/ClusterTreeOutput.cpp
src/ClustalW/src/tree/ClusterTreeOutput.h
src/ClustalW/src/tree/NJTree.cpp
src/ClustalW/src/tree/NJTree.h
src/ClustalW/src/tree/RandomGenerator.cpp
src/ClustalW/src/tree/RandomGenerator.h
src/ClustalW/src/tree/Tree.cpp
src/ClustalW/src/tree/Tree.h
src/ClustalW/src/tree/TreeInterface.cpp
src/ClustalW/src/tree/TreeInterface.h
src/ClustalW/src/tree/UPGMA
src/ClustalW/src/tree/UPGMA/Node.cpp
src/ClustalW/src/tree/UPGMA/Node.h
src/ClustalW/src/tree/UPGMA/RootedClusterTree.cpp
src/ClustalW/src/tree/UPGMA/RootedClusterTree.h
src/ClustalW/src/tree/UPGMA/RootedGuideTree.cpp
src/ClustalW/src/tree/UPGMA/RootedGuideTree.h
src/ClustalW/src/tree/UPGMA/RootedTreeOutput.cpp
src/ClustalW/src/tree/UPGMA/RootedTreeOutput.h
src/ClustalW/src/tree/UPGMA/UPGMAAlgorithm.cpp
src/ClustalW/src/tree/UPGMA/UPGMAAlgorithm.h
src/ClustalW/src/tree/UPGMA/upgmadata.h
src/ClustalW/src/tree/UnRootedClusterTree.cpp
src/ClustalW/src/tree/UnRootedClusterTree.h
src/ClustalW/src/tree/dayhoff.h
src/ClustalW/windows
src/ClustalW/windows/Makefile
src/ClustalW/windows/m4
src/ClustalW/windows/m4/Makefile
src/ClustalW/windows/src
src/ClustalW/windows/src/Makefile
src/ClustalW/windows/src/clustalw_version.h
src/ClustalW/windows/src/config.h
src/Makevars
src/Makevars.win
src/Muscle
src/Muscle/Makefile
src/Muscle/README.txt
src/Muscle/RMuscle.cpp
src/Muscle/RMuscle.h
src/Muscle/aligngivenpath.cpp
src/Muscle/aligngivenpathsw.cpp
src/Muscle/aligntwomsas.cpp
src/Muscle/aligntwoprofs.cpp
src/Muscle/aln.cpp
src/Muscle/alpha.cpp
src/Muscle/alpha.h
src/Muscle/anchors.cpp
src/Muscle/bittraceback.cpp
src/Muscle/blosum62.cpp
src/Muscle/blosumla.cpp
src/Muscle/clust.cpp
src/Muscle/clust.h
src/Muscle/cluster.cpp
src/Muscle/cluster.h
src/Muscle/clustset.h
src/Muscle/clustsetdf.h
src/Muscle/clustsetmsa.h
src/Muscle/clwwt.cpp
src/Muscle/color.cpp
src/Muscle/cons.cpp
src/Muscle/diaglist.cpp
src/Muscle/diaglist.h
src/Muscle/diffobjscore.cpp
src/Muscle/diffpaths.cpp
src/Muscle/difftrees.cpp
src/Muscle/difftreese.cpp
src/Muscle/distcalc.cpp
src/Muscle/distcalc.h
src/Muscle/distfunc.cpp
src/Muscle/distfunc.h
src/Muscle/distpwkimura.cpp
src/Muscle/domuscle.cpp
src/Muscle/dosp.cpp
src/Muscle/dpregionlist.h
src/Muscle/dpreglist.cpp
src/Muscle/dpreglist.h
src/Muscle/drawtree.cpp
src/Muscle/edgelist.cpp
src/Muscle/edgelist.h
src/Muscle/enumopts.cpp
src/Muscle/enumopts.h
src/Muscle/enums.h
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src/gc-7.2/ptr_chck.c
src/gc-7.2/real_malloc.c
src/gc-7.2/reclaim.c
src/gc-7.2/rs6000_mach_dep.s
src/gc-7.2/sparc_mach_dep.S
src/gc-7.2/sparc_netbsd_mach_dep.s
src/gc-7.2/sparc_sunos4_mach_dep.s
src/gc-7.2/specific.c
src/gc-7.2/stubborn.c
src/gc-7.2/test-driver
src/gc-7.2/tests
src/gc-7.2/tests/CMakeLists.txt
src/gc-7.2/tests/huge_test.c
src/gc-7.2/tests/initsecondarythread.c
src/gc-7.2/tests/leak_test.c
src/gc-7.2/tests/middle.c
src/gc-7.2/tests/realloc_test.c
src/gc-7.2/tests/smash_test.c
src/gc-7.2/tests/staticrootslib.c
src/gc-7.2/tests/staticrootstest.c
src/gc-7.2/tests/test.c
src/gc-7.2/tests/test_cpp.cc
src/gc-7.2/tests/tests.am
src/gc-7.2/tests/thread_leak_test.c
src/gc-7.2/tests/threadkey_test.c
src/gc-7.2/tests/trace_test.c
src/gc-7.2/thread_local_alloc.c
src/gc-7.2/typd_mlc.c
src/gc-7.2/win32_threads.c
vignettes
vignettes/JKU_EN_noName.pdf
vignettes/SweaveExample.txt
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/knitrExample.txt
vignettes/lit.bib
vignettes/msa.Rnw
vignettes/texshade.sty
msa documentation built on May 20, 2017, 10:20 p.m.

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