muscle: Multiple Sequence Alignment with MUSCLE

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MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.

Author
Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.
Date of publication
None
Maintainer
Alex T. Kalinka <alex.t.kalinka@gmail.com>
License
Unlimited
Version
3.16.0
URLs

View on Bioconductor

Man pages

muscle
Multiple Sequence Alignment
muscle-package
Multiple Sequence Alignment
umax
Unaligned MAX sequences

Files in this package

muscle/DESCRIPTION
muscle/NAMESPACE
muscle/NEWS
muscle/R
muscle/R/muscle_main.R
muscle/build
muscle/build/vignette.rds
muscle/data
muscle/data/umax.rda
muscle/inst
muscle/inst/CITATION
muscle/inst/doc
muscle/inst/doc/muscle-vignette.R
muscle/inst/doc/muscle-vignette.Rnw
muscle/inst/doc/muscle-vignette.pdf
muscle/man
muscle/man/muscle-package.Rd
muscle/man/muscle.Rd
muscle/man/umax.Rd
muscle/src
muscle/src/aligngivenpath.cpp
muscle/src/aligngivenpathsw.cpp
muscle/src/aligntwomsas.cpp
muscle/src/aligntwoprofs.cpp
muscle/src/aln.cpp
muscle/src/alpha.cpp
muscle/src/alpha.h
muscle/src/anchors.cpp
muscle/src/bittraceback.cpp
muscle/src/blosum62.cpp
muscle/src/blosumla.cpp
muscle/src/clust.cpp
muscle/src/clust.h
muscle/src/cluster.cpp
muscle/src/cluster.h
muscle/src/clustset.h
muscle/src/clustsetdf.h
muscle/src/clustsetmsa.h
muscle/src/clwwt.cpp
muscle/src/color.cpp
muscle/src/cons.cpp
muscle/src/diaglist.cpp
muscle/src/diaglist.h
muscle/src/diffobjscore.cpp
muscle/src/diffpaths.cpp
muscle/src/difftrees.cpp
muscle/src/difftreese.cpp
muscle/src/distcalc.cpp
muscle/src/distcalc.h
muscle/src/distfunc.cpp
muscle/src/distfunc.h
muscle/src/distpwkimura.cpp
muscle/src/domuscle.cpp
muscle/src/dosp.cpp
muscle/src/dpregionlist.h
muscle/src/dpreglist.cpp
muscle/src/dpreglist.h
muscle/src/drawtree.cpp
muscle/src/edgelist.cpp
muscle/src/edgelist.h
muscle/src/enumopts.cpp
muscle/src/enumopts.h
muscle/src/enums.h
muscle/src/enumtostr.cpp
muscle/src/estring.cpp
muscle/src/estring.h
muscle/src/fasta.cpp
muscle/src/fasta2.cpp
muscle/src/fastclust.cpp
muscle/src/fastdist.cpp
muscle/src/fastdistjones.cpp
muscle/src/fastdistkbit.cpp
muscle/src/fastdistkmer.cpp
muscle/src/fastdistmafft.cpp
muscle/src/fastdistnuc.cpp
muscle/src/fastscorepath2.cpp
muscle/src/finddiags.cpp
muscle/src/finddiagsn.cpp
muscle/src/gapscoredimer.h
muscle/src/glbalign.cpp
muscle/src/glbalign352.cpp
muscle/src/glbaligndiag.cpp
muscle/src/glbalignla.cpp
muscle/src/glbalignle.cpp
muscle/src/glbalignns.cpp
muscle/src/glbalignsimple.cpp
muscle/src/glbalignsp.cpp
muscle/src/glbalignspn.cpp
muscle/src/glbalignss.cpp
muscle/src/glbalndimer.cpp
muscle/src/globals.cpp
muscle/src/globalslinux.cpp
muscle/src/globalsosx.cpp
muscle/src/globalsother.cpp
muscle/src/globalswin32.cpp
muscle/src/gonnet.cpp
muscle/src/gonnet.h
muscle/src/gotowt.cpp
muscle/src/henikoffweight.cpp
muscle/src/henikoffweightpb.cpp
muscle/src/html.cpp
muscle/src/hydro.cpp
muscle/src/intmath.cpp
muscle/src/intmath.h
muscle/src/local.cpp
muscle/src/main.cpp
muscle/src/makerootmsa.cpp
muscle/src/makerootmsab.cpp
muscle/src/maketree.cpp
muscle/src/mhack.cpp
muscle/src/mpam200.cpp
muscle/src/msa.cpp
muscle/src/msa.h
muscle/src/msa2.cpp
muscle/src/msadist.h
muscle/src/msadistkimura.cpp
muscle/src/msadistkimura.h
muscle/src/msadistmafft.h
muscle/src/msf.cpp
muscle/src/muscle.cpp
muscle/src/muscle.h
muscle/src/muscleout.cpp
muscle/src/nucmx.cpp
muscle/src/nwdasimple.cpp
muscle/src/nwdasimple2.cpp
muscle/src/nwdasmall.cpp
muscle/src/nwrec.cpp
muscle/src/nwsmall.cpp
muscle/src/objscore.cpp
muscle/src/objscore.h
muscle/src/objscore2.cpp
muscle/src/objscoreda.cpp
muscle/src/onexception.cpp
muscle/src/optionsR.cpp
muscle/src/outweights.cpp
muscle/src/pam200mafft.cpp
muscle/src/params.cpp
muscle/src/params.h
muscle/src/phy.cpp
muscle/src/phy2.cpp
muscle/src/phy3.cpp
muscle/src/phy4.cpp
muscle/src/phyfromclust.cpp
muscle/src/phyfromfile.cpp
muscle/src/physeq.cpp
muscle/src/phytofile.cpp
muscle/src/posgap.cpp
muscle/src/ppscore.cpp
muscle/src/profdb.cpp
muscle/src/profile.cpp
muscle/src/profile.h
muscle/src/profilefrommsa.cpp
muscle/src/progalign.cpp
muscle/src/progress.cpp
muscle/src/progressivealign.cpp
muscle/src/pwpath.cpp
muscle/src/pwpath.h
muscle/src/readmx.cpp
muscle/src/realigndiffs.cpp
muscle/src/realigndiffse.cpp
muscle/src/redblack.cpp
muscle/src/refine.cpp
muscle/src/refinehoriz.cpp
muscle/src/refinesubfams.cpp
muscle/src/refinetree.cpp
muscle/src/refinetreee.cpp
muscle/src/refinevert.cpp
muscle/src/refinew.cpp
muscle/src/savebest.cpp
muscle/src/scoredist.cpp
muscle/src/scoregaps.cpp
muscle/src/scorehistory.cpp
muscle/src/scorehistory.h
muscle/src/scorepp.cpp
muscle/src/seq.cpp
muscle/src/seq.h
muscle/src/seqvect.cpp
muscle/src/seqvect.h
muscle/src/setblosumweights.cpp
muscle/src/setgscweights.cpp
muscle/src/setnewhandler.cpp
muscle/src/spfast.cpp
muscle/src/sptest.cpp
muscle/src/stabilize.cpp
muscle/src/subfam.cpp
muscle/src/subfams.cpp
muscle/src/svnmods.h
muscle/src/svnversion.h
muscle/src/sw.cpp
muscle/src/termgaps.cpp
muscle/src/textfile.cpp
muscle/src/textfile.h
muscle/src/threewaywt.cpp
muscle/src/timing.h
muscle/src/tomhydro.cpp
muscle/src/traceback.cpp
muscle/src/tracebackopt.cpp
muscle/src/tracebacksw.cpp
muscle/src/tree.h
muscle/src/treefrommsa.cpp
muscle/src/types.h
muscle/src/typetostr.cpp
muscle/src/unixio.h
muscle/src/upgma2.cpp
muscle/src/usage.cpp
muscle/src/validateids.cpp
muscle/src/vtml2.cpp
muscle/src/writescorefile.cpp
muscle/vignettes
muscle/vignettes/muscle-vignette.Rnw