Files in msa
Multiple Sequence Alignment

NAMESPACE
cleanup.win
cleanup
DESCRIPTION
man/msa.Rd man/MsaMetaData-class.Rd man/msa-package.Rd man/msaConsensusSequence-methods.Rd man/msaMuscle.Rd man/msaConservationScore-methods.Rd man/MsaMultipleAlignmentClasses.Rd man/msaConvert.Rd man/msaCheckNames.Rd man/msaClustalOmega.Rd man/msaClustalW.Rd man/msaPrettyPrint.Rd R/msaConsensusSequence-methods.R R/AllClasses.R R/msaCheckNames.R R/show-methods.R R/version-methods.R R/msaConservationScore-methods.R R/msaClustalOmega.R R/helperFunctions.R R/msaConvert.R R/convertRows.R R/print-methods.R R/msaMuscle.R R/inputChecks.R R/AllGenerics.R R/msaClustalW.R R/msaPrettyPrint.R R/params-methods.R R/msa.R
inst/COPYRIGHT
inst/NEWS
inst/CITATION
inst/tex/texshade.sty
inst/extdata/msaMuscleHelp.txt
inst/extdata/msaHelpPrefix.txt
inst/extdata/msaClustalOmegaHelp.txt
inst/extdata/msaCommonHelp.txt
inst/extdata/msaClustalWHelp.txt
inst/examples/exampleRNA.fasta
inst/examples/HemoglobinAA.fasta
inst/examples/exampleDNA.fasta
inst/examples/exampleAA.fasta
inst/doc/msa.Rnw
inst/doc/msa.pdf inst/doc/msa.R
build/vignette.rds
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/lit.bib
vignettes/bioinf-article.txi
vignettes/knitrExample.txt
vignettes/texshade.sty
vignettes/msa.Rnw
vignettes/JKU_EN_noName.pdf
vignettes/SweaveExample.txt
src/Makevars.win
src/SplitCharVector2List.cpp
src/R_init_msa.cpp
src/SplitCharVector2List.h
src/SplitCharVector2Matrix.cpp
src/Makevars
src/SplitCharVector2Matrix.h
src/ClustalOmega/ltmain.sh
src/ClustalOmega/Doxyfile.in
src/ClustalOmega/AUTHORS
src/ClustalOmega/COPYING
src/ClustalOmega/depcomp
src/ClustalOmega/missing
src/ClustalOmega/config.sub
src/ClustalOmega/msaMakefile.win
src/ClustalOmega/configure.ac
src/ClustalOmega/config.guess
src/ClustalOmega/Makefile.am
src/ClustalOmega/configure
src/ClustalOmega/Doxyfile
src/ClustalOmega/Makefile.in
src/ClustalOmega/install-sh
src/ClustalOmega/msaMakefile
src/ClustalOmega/aclocal.m4
src/ClustalOmega/clustalo.pc.in
src/ClustalOmega/src/main.cpp
src/ClustalOmega/src/config.h.in
src/ClustalOmega/src/RClustalOmega.cpp
src/ClustalOmega/src/RClustalOmega.h
src/ClustalOmega/src/clustalo-api-test.c
src/ClustalOmega/src/mymain.h
src/ClustalOmega/src/clustal-omega.h
src/ClustalOmega/src/clustal-omega-config.h
src/ClustalOmega/src/Makefile.in
src/ClustalOmega/src/clustal-omega.c
src/ClustalOmega/src/Makefile.am
src/ClustalOmega/src/mymain.c
src/ClustalOmega/src/hhalign/hhfunc-C.h
src/ClustalOmega/src/hhalign/hhfullalignment.h
src/ClustalOmega/src/hhalign/Makefile.am
src/ClustalOmega/src/hhalign/hhhmm-C.h
src/ClustalOmega/src/hhalign/hhalignment.h
src/ClustalOmega/src/hhalign/list-C.h
src/ClustalOmega/src/hhalign/util-C.h
src/ClustalOmega/src/hhalign/hhfullalignment-C.h
src/ClustalOmega/src/hhalign/hhhit.h
src/ClustalOmega/src/hhalign/Makefile.in
src/ClustalOmega/src/hhalign/hhhitlist.h
src/ClustalOmega/src/hhalign/hhalignment-C.h
src/ClustalOmega/src/hhalign/hash.h
src/ClustalOmega/src/hhalign/list.h
src/ClustalOmega/src/hhalign/general.h
src/ClustalOmega/src/hhalign/hhfunc.h
src/ClustalOmega/src/hhalign/hhhitlist-C.h
src/ClustalOmega/src/hhalign/hhutil-C.h
src/ClustalOmega/src/hhalign/hhhit-C.h
src/ClustalOmega/src/hhalign/hhdecl-C.h
src/ClustalOmega/src/hhalign/hhhalfalignment.h
src/ClustalOmega/src/hhalign/hhhmm.h
src/ClustalOmega/src/hhalign/hhalign.cpp
src/ClustalOmega/src/hhalign/hhhalfalignment-C.h
src/ClustalOmega/src/hhalign/hhmatrices-C.h
src/ClustalOmega/src/hhalign/hhalign.h
src/ClustalOmega/src/hhalign/hash-C.h
src/ClustalOmega/src/squid/a2m.c
src/ClustalOmega/src/squid/sre_math.c
src/ClustalOmega/src/squid/gki.h
src/ClustalOmega/src/squid/getopt.c
src/ClustalOmega/src/squid/dayhoff.c
src/ClustalOmega/src/squid/gsi.c
src/ClustalOmega/src/squid/msf.c
src/ClustalOmega/src/squid/sre_string.c
src/ClustalOmega/src/squid/msa.h
src/ClustalOmega/src/squid/clustal.c
src/ClustalOmega/src/squid/vectorops.c
src/ClustalOmega/src/squid/stopwatch.c
src/ClustalOmega/src/squid/file.c
src/ClustalOmega/src/squid/eps.c
src/ClustalOmega/src/squid/squidcore.c
src/ClustalOmega/src/squid/aligneval.c
src/ClustalOmega/src/squid/weight.c
src/ClustalOmega/src/squid/sre_random.c
src/ClustalOmega/src/squid/rk.h
src/ClustalOmega/src/squid/gsi64.h
src/ClustalOmega/src/squid/LICENSE
src/ClustalOmega/src/squid/ssi.c
src/ClustalOmega/src/squid/types.c
src/ClustalOmega/src/squid/hsregex.c
src/ClustalOmega/src/squid/stockholm.h
src/ClustalOmega/src/squid/squid.h
src/ClustalOmega/src/squid/sre_ctype.c
src/ClustalOmega/src/squid/cluster.c
src/ClustalOmega/src/squid/sqfuncs.h
src/ClustalOmega/src/squid/iupac.c
src/ClustalOmega/src/squid/vectorops.h
src/ClustalOmega/src/squid/stopwatch.h
src/ClustalOmega/src/squid/shuffle.c
src/ClustalOmega/src/squid/msa.c
src/ClustalOmega/src/squid/Makefile.am
src/ClustalOmega/src/squid/translate.c
src/ClustalOmega/src/squid/sqio.c
src/ClustalOmega/src/squid/sqerror.c
src/ClustalOmega/src/squid/gsi.h
src/ClustalOmega/src/squid/COPYRIGHT
src/ClustalOmega/src/squid/gki.c
src/ClustalOmega/src/squid/alignio.c
src/ClustalOmega/src/squid/Makefile.in
src/ClustalOmega/src/squid/clustalo.README
src/ClustalOmega/src/squid/phylip.c
src/ClustalOmega/src/squid/00README
src/ClustalOmega/src/squid/stockholm.c
src/ClustalOmega/src/squid/squid-1.9g.tar.gz
src/ClustalOmega/src/squid/version.h
src/ClustalOmega/src/squid/seqencode.c
src/ClustalOmega/src/squid/gsi64.c
src/ClustalOmega/src/squid/ssi.h
src/ClustalOmega/src/squid/selex.c
src/ClustalOmega/src/squid/stack.c
src/ClustalOmega/src/squid/revcomp.c
src/ClustalOmega/src/squid/sre_random.h
src/ClustalOmega/src/squid/rk.c
src/ClustalOmega/src/kmpp/KmTree.h
src/ClustalOmega/src/kmpp/KMeans.cpp
src/ClustalOmega/src/kmpp/KmUtils.h
src/ClustalOmega/src/kmpp/KMeans.h
src/ClustalOmega/src/kmpp/KmUtils.cpp
src/ClustalOmega/src/kmpp/KmTree.cpp
src/ClustalOmega/src/kmpp/Makefile.am
src/ClustalOmega/src/kmpp/Makefile.in
src/ClustalOmega/src/argtable2/arg_date.c
src/ClustalOmega/src/argtable2/getopt.h
src/ClustalOmega/src/argtable2/CMakeLists.txt
src/ClustalOmega/src/argtable2/arg_file.c
src/ClustalOmega/src/argtable2/config.h
src/ClustalOmega/src/argtable2/arg_lit.c
src/ClustalOmega/src/argtable2/argtable2.c
src/ClustalOmega/src/argtable2/config.h.in
src/ClustalOmega/src/argtable2/arg_dbl.c
src/ClustalOmega/src/argtable2/getopt.c
src/ClustalOmega/src/argtable2/argtable2.def
src/ClustalOmega/src/argtable2/Makefile.am
src/ClustalOmega/src/argtable2/arg_int.c
src/ClustalOmega/src/argtable2/argtable2.h
src/ClustalOmega/src/argtable2/Makefile.in
src/ClustalOmega/src/argtable2/Makefile.nmake
src/ClustalOmega/src/argtable2/arg_end.c
src/ClustalOmega/src/argtable2/arg_rem.c
src/ClustalOmega/src/argtable2/getopt1.c
src/ClustalOmega/src/argtable2/arg_str.c
src/ClustalOmega/src/argtable2/arg_rex.c
src/ClustalOmega/src/clustal/mbed.h
src/ClustalOmega/src/clustal/list.h
src/ClustalOmega/src/clustal/symmatrix.h
src/ClustalOmega/src/clustal/hhalign_wrapper.h
src/ClustalOmega/src/clustal/seq.c
src/ClustalOmega/src/clustal/tree.c
src/ClustalOmega/src/clustal/ktuple_pair.h
src/ClustalOmega/src/clustal/progress.c
src/ClustalOmega/src/clustal/pair_dist.c
src/ClustalOmega/src/clustal/log.c
src/ClustalOmega/src/clustal/muscle_upgma.h
src/ClustalOmega/src/clustal/muscle_tree.c
src/ClustalOmega/src/clustal/weights.h
src/ClustalOmega/src/clustal/util.h
src/ClustalOmega/src/clustal/seq.h
src/ClustalOmega/src/clustal/tree.h
src/ClustalOmega/src/clustal/Makefile.in
src/ClustalOmega/src/clustal/queue.h
src/ClustalOmega/src/clustal/symmatrix.c
src/ClustalOmega/src/clustal/hhalign_wrapper.c
src/ClustalOmega/src/clustal/mbed.c
src/ClustalOmega/src/clustal/list.c
src/ClustalOmega/src/clustal/util.c
src/ClustalOmega/src/clustal/Makefile.am
src/ClustalOmega/src/clustal/weights.c
src/ClustalOmega/src/clustal/muscle_tree.h
src/ClustalOmega/src/clustal/ktuple_pair.c
src/ClustalOmega/src/clustal/progress.h
src/ClustalOmega/src/clustal/pair_dist.h
src/ClustalOmega/src/clustal/log.h
src/ClustalOmega/src/clustal/muscle_upgma.c
src/ClustalOmega/src/exceptions4c/Makefile.am
src/ClustalOmega/src/exceptions4c/e4c_lite.c
src/ClustalOmega/src/exceptions4c/Makefile.in
src/ClustalOmega/src/exceptions4c/config.h
src/ClustalOmega/src/exceptions4c/e4c_lite.h
src/ClustalOmega/src/exceptions4c/config.h.in
src/ClustalOmega/windows/src/config.h
src/ClustalOmega/windows/src/clustal-omega-config.h
src/ClustalOmega/m4/libtool.m4
src/ClustalOmega/m4/ax_prefix_config_h.m4
src/ClustalOmega/m4/ltversion.m4
src/ClustalOmega/m4/ltoptions.m4
src/ClustalOmega/m4/ltsugar.m4
src/ClustalOmega/m4/ax_openmp.m4
src/Muscle/scorehistory.h
src/Muscle/objscore2.cpp
src/Muscle/subfam.cpp
src/Muscle/gonnet.h
src/Muscle/phy4.cpp
src/Muscle/dosp.cpp
src/Muscle/blosum62.cpp
src/Muscle/local.cpp
src/Muscle/msaMakefile
src/Muscle/edgelist.cpp
src/Muscle/nwrec.cpp
src/Muscle/progalign.cpp
src/Muscle/phy3.cpp
src/Muscle/gotowt.cpp
src/Muscle/msadistmafft.h
src/Muscle/phyfromclust.cpp
src/Muscle/mpam200.cpp
src/Muscle/make.out
src/Muscle/html.cpp
src/Muscle/gatest.cpp
src/Muscle/muscle.h
src/Muscle/setblosumweights.cpp
src/Muscle/makerootmsa.cpp
src/Muscle/tracebackopt.cpp
src/Muscle/main.cpp
src/Muscle/globalslinux.cpp
src/Muscle/progressivealign.cpp
src/Muscle/estring.h
src/Muscle/fastdistjones.cpp
src/Muscle/traceback.cpp
src/Muscle/glbalignsimple.cpp
src/Muscle/blosumla.cpp
src/Muscle/glbalignspn.cpp
src/Muscle/posgap.cpp
src/Muscle/params.cpp
src/Muscle/typetostr.cpp
src/Muscle/diaglist.cpp
src/Muscle/estring.cpp
src/Muscle/aligngivenpathsw.cpp
src/Muscle/params.h
src/Muscle/clwwt.cpp
src/Muscle/fastdistkmer.cpp
src/Muscle/phyfromfile.cpp
src/Muscle/hydro.cpp
src/Muscle/README.txt
src/Muscle/mk
src/Muscle/scoremx.cpp
src/Muscle/seqvect.h
src/Muscle/fastdistkbit.cpp
src/Muscle/msa.h
src/Muscle/svnmods.h
src/Muscle/diaglist.h
src/Muscle/intmath.cpp
src/Muscle/makerootmsab.cpp
src/Muscle/glbalign352.cpp
src/Muscle/msaMakefile.win
src/Muscle/seq.h
src/Muscle/glbaligndiag.cpp
src/Muscle/domuscle.cpp
src/Muscle/maketree.cpp
src/Muscle/phy2.cpp
src/Muscle/cons.cpp
src/Muscle/intmath.h
src/Muscle/sw.cpp
src/Muscle/threewaywt.cpp
src/Muscle/dpreglist.cpp
src/Muscle/phytofile.cpp
src/Muscle/glbalignsp.cpp
src/Muscle/globalswin32.cpp
src/Muscle/fastdistmafft.cpp
src/Muscle/edgelist.h
src/Muscle/clustsetmsa.h
src/Muscle/mhack.cpp
src/Muscle/svnversion.h
src/Muscle/scorepp.cpp
src/Muscle/clust.cpp
src/Muscle/fastdistnuc.cpp
src/Muscle/nwsmall.cpp
src/Muscle/distpwkimura.cpp
src/Muscle/difftreese.cpp
src/Muscle/henikoffweightpb.cpp
src/Muscle/fasta.cpp
src/Muscle/diffpaths.cpp
src/Muscle/distfunc.h
src/Muscle/glbalignla.cpp
src/Muscle/globalsother.cpp
src/Muscle/distcalc.h
src/Muscle/stabilize.cpp
src/Muscle/physeq.cpp
src/Muscle/aligntwomsas.cpp
src/Muscle/timing.h
src/Muscle/scoregaps.cpp
src/Muscle/msf.cpp
src/Muscle/gapscoredimer.h
src/Muscle/diffobjscore.cpp
src/Muscle/globals.cpp
src/Muscle/tracebacksw.cpp
src/Muscle/msa.cpp
src/Muscle/objscore.h
src/Muscle/profdb.cpp
src/Muscle/enumopts.h
src/Muscle/refinew.cpp
src/Muscle/fasta2.cpp
src/Muscle/refinesubfams.cpp
src/Muscle/glbalign.cpp
src/Muscle/usage.cpp
src/Muscle/glbalignle.cpp
src/Muscle/unixio.h
src/Muscle/alpha.h
src/Muscle/seqvect.cpp
src/Muscle/progress.cpp
src/Muscle/setnewhandler.cpp
src/Muscle/pam200mafft.cpp
src/Muscle/nwdasimple.cpp
src/Muscle/seq.cpp
src/Muscle/realigndiffs.cpp
src/Muscle/termgaps.cpp
src/Muscle/msadistkimura.cpp
src/Muscle/upgma2.cpp
src/Muscle/color.cpp
src/Muscle/RMuscle.cpp
src/Muscle/finddiags.cpp
src/Muscle/finddiagsn.cpp
src/Muscle/bittraceback.cpp
src/Muscle/redblack.cpp
src/Muscle/clustsetdf.h
src/Muscle/nucmx.cpp
src/Muscle/distcalc.cpp
src/Muscle/refinevert.cpp
src/Muscle/validateids.cpp
src/Muscle/gonnet.cpp
src/Muscle/subfams.cpp
src/Muscle/cluster.h
src/Muscle/treefrommsa.cpp
src/Muscle/glbalignns.cpp
src/Muscle/make.err
src/Muscle/refine.cpp
src/Muscle/enums.h
src/Muscle/ppscore.cpp
src/Muscle/scoredist.cpp
src/Muscle/profilefrommsa.cpp
src/Muscle/vtml2.cpp
src/Muscle/textfile.cpp
src/Muscle/setgscweights.cpp
src/Muscle/anchors.cpp
src/Muscle/Makefile
src/Muscle/types.h
src/Muscle/glbalignss.cpp
src/Muscle/msadistkimura.h
src/Muscle/pwpath.cpp
src/Muscle/fastscorepath2.cpp
src/Muscle/cluster.cpp
src/Muscle/clustset.h
src/Muscle/alpha.cpp
src/Muscle/aligntwoprofs.cpp
src/Muscle/readmx.cpp
src/Muscle/dpreglist.h
src/Muscle/msadist.h
src/Muscle/drawtree.cpp
src/Muscle/enumopts.cpp
src/Muscle/difftrees.cpp
src/Muscle/tomhydro.cpp
src/Muscle/globalsosx.cpp
src/Muscle/onexception.cpp
src/Muscle/realigndiffse.cpp
src/Muscle/options.cpp
src/Muscle/muscle.cpp
src/Muscle/objscore.cpp
src/Muscle/releases.txt
src/Muscle/dpregionlist.h
src/Muscle/scorehistory.cpp
src/Muscle/muscleout.cpp
src/Muscle/objscoreda.cpp
src/Muscle/aligngivenpath.cpp
src/Muscle/fastclust.cpp
src/Muscle/version.txt
src/Muscle/phy.cpp
src/Muscle/nwdasimple2.cpp
src/Muscle/outweights.cpp
src/Muscle/tree.h
src/Muscle/savebest.cpp
src/Muscle/RMuscle.h
src/Muscle/aln.cpp
src/Muscle/pwpath.h
src/Muscle/profile.h
src/Muscle/refinehoriz.cpp
src/Muscle/profile.cpp
src/Muscle/distfunc.cpp
src/Muscle/clust.h
src/Muscle/refinetree.cpp
src/Muscle/henikoffweight.cpp
src/Muscle/textfile.h
src/Muscle/refinetreee.cpp
src/Muscle/nwdasmall.cpp
src/Muscle/spfast.cpp
src/Muscle/sptest.cpp
src/Muscle/msa2.cpp
src/Muscle/glbalndimer.cpp
src/Muscle/enumtostr.cpp
src/Muscle/writescorefile.cpp
src/Muscle/fastdist.cpp
src/gc-7.2/checksums.c
src/gc-7.2/PCR-Makefile
src/gc-7.2/mips_sgi_mach_dep.s
src/gc-7.2/mark.c
src/gc-7.2/Makefile.am
src/gc-7.2/obj_map.c
src/gc-7.2/stubborn.c
src/gc-7.2/darwin_stop_world.c
src/gc-7.2/reclaim.c
src/gc-7.2/ltmain.sh
src/gc-7.2/WCC_MAKEFILE
src/gc-7.2/alpha_mach_dep.S
src/gc-7.2/config.guess
src/gc-7.2/allchblk.c
src/gc-7.2/mkinstalldirs
src/gc-7.2/pcr_interface.c
src/gc-7.2/pthread_support.c
src/gc-7.2/misc.c
src/gc-7.2/specific.c
src/gc-7.2/install-sh
src/gc-7.2/gc_cpp.cpp
src/gc-7.2/callprocs
src/gc-7.2/test-driver
src/gc-7.2/backgraph.c
src/gc-7.2/mips_ultrix_mach_dep.s
src/gc-7.2/depcomp
src/gc-7.2/missing
src/gc-7.2/aclocal.m4
src/gc-7.2/gc_dlopen.c
src/gc-7.2/mallocx.c
src/gc-7.2/bdw-gc.pc.in
src/gc-7.2/typd_mlc.c
src/gc-7.2/dyn_load.c
src/gc-7.2/ia64_save_regs_in_stack.s
src/gc-7.2/NT_MAKEFILE
src/gc-7.2/Makefile.in
src/gc-7.2/EMX_MAKEFILE
src/gc-7.2/mach_dep.c
src/gc-7.2/malloc.c
src/gc-7.2/Makefile.DLLs
src/gc-7.2/NT_STATIC_THREADS_MAKEFILE
src/gc-7.2/real_malloc.c
src/gc-7.2/Makefile.direct
src/gc-7.2/build_atomic_ops.sh.cygwin
src/gc-7.2/msaMakefile
src/gc-7.2/sparc_sunos4_mach_dep.s
src/gc-7.2/thread_local_alloc.c
src/gc-7.2/compile
src/gc-7.2/finalize.c
src/gc-7.2/NT_X64_THREADS_MAKEFILE
src/gc-7.2/build_atomic_ops.sh
src/gc-7.2/new_hblk.c
src/gc-7.2/alloc.c
src/gc-7.2/MacProjects.sit.hqx
src/gc-7.2/pthread_stop_world.c
src/gc-7.2/pthread_start.c
src/gc-7.2/msaMakefile.win
src/gc-7.2/dbg_mlc.c
src/gc-7.2/BCC_MAKEFILE
src/gc-7.2/ChangeLog
src/gc-7.2/config.sub
src/gc-7.2/ptr_chck.c
src/gc-7.2/rs6000_mach_dep.s src/gc-7.2/sparc_mach_dep.S
src/gc-7.2/mark_rts.c
src/gc-7.2/Makefile.dj
src/gc-7.2/configure
src/gc-7.2/README.QUICK
src/gc-7.2/CMakeLists.txt
src/gc-7.2/blacklst.c
src/gc-7.2/OS2_MAKEFILE
src/gc-7.2/gcj_mlc.c
src/gc-7.2/autogen.sh
src/gc-7.2/sparc_netbsd_mach_dep.s
src/gc-7.2/gc_cpp.cc
src/gc-7.2/configure.host
src/gc-7.2/SMakefile.amiga
src/gc-7.2/configure.ac
src/gc-7.2/os_dep.c
src/gc-7.2/win32_threads.c
src/gc-7.2/headers.c
src/gc-7.2/gc.mak
src/gc-7.2/digimars.mak
src/gc-7.2/NT_X64_STATIC_THREADS_MAKEFILE
src/gc-7.2/include/gc_typed.h
src/gc-7.2/include/gc_cpp.h
src/gc-7.2/include/new_gc_alloc.h
src/gc-7.2/include/gc_version.h
src/gc-7.2/include/leak_detector.h
src/gc-7.2/include/gc_config_macros.h
src/gc-7.2/include/cord.h
src/gc-7.2/include/gc_mark.h
src/gc-7.2/include/gc_gcj.h
src/gc-7.2/include/weakpointer.h
src/gc-7.2/include/gc_pthread_redirects.h
src/gc-7.2/include/gc_allocator.h
src/gc-7.2/include/gc_amiga_redirects.h
src/gc-7.2/include/gc_inline.h
src/gc-7.2/include/javaxfc.h
src/gc-7.2/include/gc_backptr.h
src/gc-7.2/include/ec.h
src/gc-7.2/include/gc.h
src/gc-7.2/include/gc_tiny_fl.h
src/gc-7.2/include/include.am
src/gc-7.2/include/extra/gc.h
src/gc-7.2/include/extra/gc_cpp.h
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msa documentation built on Nov. 17, 2017, 8:22 a.m.