msa: Multiple Sequence Alignment

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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.

Author
Enrico Bonatesta, Christoph Horejs-Kainrath, Ulrich Bodenhofer
Date of publication
None
Maintainer
Ulrich Bodenhofer <bodenhofer@bioinf.jku.at>
License
GPL (>= 2)
Version
1.6.0
URLs

View on Bioconductor

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
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

Files in this package

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
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msa/src/Muscle/difftreese.cpp
msa/src/Muscle/distcalc.cpp
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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
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msa/src/Muscle/msadistmafft.h
msa/src/Muscle/msf.cpp
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msa/src/Muscle/nwrec.cpp
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msa/src/Muscle/posgap.cpp
msa/src/Muscle/ppscore.cpp
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msa/src/Muscle/refinesubfams.cpp
msa/src/Muscle/refinetree.cpp
msa/src/Muscle/refinetreee.cpp
msa/src/Muscle/refinevert.cpp
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msa/src/Muscle/scorehistory.cpp
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