muscle: Multiple Sequence Alignment with MUSCLE
Version 3.18.0

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

AuthorAlgorithm by Robert C. Edgar. R port by Alex T. Kalinka.
Bioconductor views Alignment DataImport Genetics MultipleSequenceAlignment SequenceMatching Sequencing
Date of publicationNone
MaintainerAlex T. Kalinka <alex.t.kalinka@gmail.com>
LicenseUnlimited
Version3.18.0
URL http://www.drive5.com/muscle/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("muscle")

Getting started

Package overview

Popular man pages

muscle: Multiple Sequence Alignment
muscle-package: Multiple Sequence Alignment
umax: Unaligned MAX sequences
See all...

All man pages Function index File listing

Man pages

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

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/muscle_main.R
build
build/vignette.rds
data
data/umax.rda
inst
inst/CITATION
inst/doc
inst/doc/muscle-vignette.R
inst/doc/muscle-vignette.Rnw
inst/doc/muscle-vignette.pdf
man
man/muscle-package.Rd
man/muscle.Rd
man/umax.Rd
src
src/aligngivenpath.cpp
src/aligngivenpathsw.cpp
src/aligntwomsas.cpp
src/aligntwoprofs.cpp
src/aln.cpp
src/alpha.cpp
src/alpha.h
src/anchors.cpp
src/bittraceback.cpp
src/blosum62.cpp
src/blosumla.cpp
src/clust.cpp
src/clust.h
src/cluster.cpp
src/cluster.h
src/clustset.h
src/clustsetdf.h
src/clustsetmsa.h
src/clwwt.cpp
src/color.cpp
src/cons.cpp
src/diaglist.cpp
src/diaglist.h
src/diffobjscore.cpp
src/diffpaths.cpp
src/difftrees.cpp
src/difftreese.cpp
src/distcalc.cpp
src/distcalc.h
src/distfunc.cpp
src/distfunc.h
src/distpwkimura.cpp
src/domuscle.cpp
src/dosp.cpp
src/dpregionlist.h
src/dpreglist.cpp
src/dpreglist.h
src/drawtree.cpp
src/edgelist.cpp
src/edgelist.h
src/enumopts.cpp
src/enumopts.h
src/enums.h
src/enumtostr.cpp
src/estring.cpp
src/estring.h
src/fasta.cpp
src/fasta2.cpp
src/fastclust.cpp
src/fastdist.cpp
src/fastdistjones.cpp
src/fastdistkbit.cpp
src/fastdistkmer.cpp
src/fastdistmafft.cpp
src/fastdistnuc.cpp
src/fastscorepath2.cpp
src/finddiags.cpp
src/finddiagsn.cpp
src/gapscoredimer.h
src/glbalign.cpp
src/glbalign352.cpp
src/glbaligndiag.cpp
src/glbalignla.cpp
src/glbalignle.cpp
src/glbalignns.cpp
src/glbalignsimple.cpp
src/glbalignsp.cpp
src/glbalignspn.cpp
src/glbalignss.cpp
src/glbalndimer.cpp
src/globals.cpp
src/globalslinux.cpp
src/globalsosx.cpp
src/globalsother.cpp
src/globalswin32.cpp
src/gonnet.cpp
src/gonnet.h
src/gotowt.cpp
src/henikoffweight.cpp
src/henikoffweightpb.cpp
src/html.cpp
src/hydro.cpp
src/intmath.cpp
src/intmath.h
src/local.cpp
src/main.cpp
src/makerootmsa.cpp
src/makerootmsab.cpp
src/maketree.cpp
src/mhack.cpp
src/mpam200.cpp
src/msa.cpp
src/msa.h
src/msa2.cpp
src/msadist.h
src/msadistkimura.cpp
src/msadistkimura.h
src/msadistmafft.h
src/msf.cpp
src/muscle.cpp
src/muscle.h
src/muscleout.cpp
src/nucmx.cpp
src/nwdasimple.cpp
src/nwdasimple2.cpp
src/nwdasmall.cpp
src/nwrec.cpp
src/nwsmall.cpp
src/objscore.cpp
src/objscore.h
src/objscore2.cpp
src/objscoreda.cpp
src/onexception.cpp
src/optionsR.cpp
src/outweights.cpp
src/pam200mafft.cpp
src/params.cpp
src/params.h
src/phy.cpp
src/phy2.cpp
src/phy3.cpp
src/phy4.cpp
src/phyfromclust.cpp
src/phyfromfile.cpp
src/physeq.cpp
src/phytofile.cpp
src/posgap.cpp
src/ppscore.cpp
src/profdb.cpp
src/profile.cpp
src/profile.h
src/profilefrommsa.cpp
src/progalign.cpp
src/progress.cpp
src/progressivealign.cpp
src/pwpath.cpp
src/pwpath.h
src/readmx.cpp
src/realigndiffs.cpp
src/realigndiffse.cpp
src/redblack.cpp
src/refine.cpp
src/refinehoriz.cpp
src/refinesubfams.cpp
src/refinetree.cpp
src/refinetreee.cpp
src/refinevert.cpp
src/refinew.cpp
src/savebest.cpp
src/scoredist.cpp
src/scoregaps.cpp
src/scorehistory.cpp
src/scorehistory.h
src/scorepp.cpp
src/seq.cpp
src/seq.h
src/seqvect.cpp
src/seqvect.h
src/setblosumweights.cpp
src/setgscweights.cpp
src/setnewhandler.cpp
src/spfast.cpp
src/sptest.cpp
src/stabilize.cpp
src/subfam.cpp
src/subfams.cpp
src/svnmods.h
src/svnversion.h
src/sw.cpp
src/termgaps.cpp
src/textfile.cpp
src/textfile.h
src/threewaywt.cpp
src/timing.h
src/tomhydro.cpp
src/traceback.cpp
src/tracebackopt.cpp
src/tracebacksw.cpp
src/tree.h
src/treefrommsa.cpp
src/types.h
src/typetostr.cpp
src/unixio.h
src/upgma2.cpp
src/usage.cpp
src/validateids.cpp
src/vtml2.cpp
src/writescorefile.cpp
vignettes
vignettes/muscle-vignette.Rnw
muscle documentation built on May 20, 2017, 9:45 p.m.

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