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Multiple Sequence Comparison by Log-Expectation.

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.gitignore
.gitignore
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
aligngivenpath.cpp
aligngivenpath.cpp
 
 
aligngivenpathsw.cpp
aligngivenpathsw.cpp
 
 
aligntwomsas.cpp
aligntwomsas.cpp
 
 
aligntwoprofs.cpp
aligntwoprofs.cpp
 
 
aln.cpp
aln.cpp
 
 
alpha.cpp
alpha.cpp
 
 
alpha.h
alpha.h
 
 
anchors.cpp
anchors.cpp
 
 
bittraceback.cpp
bittraceback.cpp
 
 
blosum62.cpp
blosum62.cpp
 
 
blosumla.cpp
blosumla.cpp
 
 
clust.cpp
clust.cpp
 
 
clust.h
clust.h
 
 
cluster.cpp
cluster.cpp
 
 
cluster.h
cluster.h
 
 
clustset.h
clustset.h
 
 
clustsetdf.h
clustsetdf.h
 
 
clustsetmsa.h
clustsetmsa.h
 
 
clwwt.cpp
clwwt.cpp
 
 
color.cpp
color.cpp
 
 
cons.cpp
cons.cpp
 
 
diaglist.cpp
diaglist.cpp
 
 
diaglist.h
diaglist.h
 
 
diffobjscore.cpp
diffobjscore.cpp
 
 
diffpaths.cpp
diffpaths.cpp
 
 
difftrees.cpp
difftrees.cpp
 
 
difftreese.cpp
difftreese.cpp
 
 
distcalc.cpp
distcalc.cpp
 
 
distcalc.h
distcalc.h
 
 
distfunc.cpp
distfunc.cpp
 
 
distfunc.h
distfunc.h
 
 
distpwkimura.cpp
distpwkimura.cpp
 
 
domuscle.cpp
domuscle.cpp
 
 
dosp.cpp
dosp.cpp
 
 
dpregionlist.h
dpregionlist.h
 
 
dpreglist.cpp
dpreglist.cpp
 
 
dpreglist.h
dpreglist.h
 
 
drawtree.cpp
drawtree.cpp
 
 
edgelist.cpp
edgelist.cpp
 
 
edgelist.h
edgelist.h
 
 
enumopts.cpp
enumopts.cpp
 
 
enumopts.h
enumopts.h
 
 
enums.h
enums.h
 
 
enumtostr.cpp
enumtostr.cpp
 
 
estring.cpp
estring.cpp
 
 
estring.h
estring.h
 
 
fasta.cpp
fasta.cpp
 
 
fasta2.cpp
fasta2.cpp
 
 
fastclust.cpp
fastclust.cpp
 
 
fastdist.cpp
fastdist.cpp
 
 
fastdistjones.cpp
fastdistjones.cpp
 
 
fastdistkbit.cpp
fastdistkbit.cpp
 
 
fastdistkmer.cpp
fastdistkmer.cpp
 
 
fastdistmafft.cpp
fastdistmafft.cpp
 
 
fastdistnuc.cpp
fastdistnuc.cpp
 
 
fastscorepath2.cpp
fastscorepath2.cpp
 
 
finddiags.cpp
finddiags.cpp
 
 
finddiagsn.cpp
finddiagsn.cpp
 
 
gapscoredimer.h
gapscoredimer.h
 
 
glbalign.cpp
glbalign.cpp
 
 
glbalign352.cpp
glbalign352.cpp
 
 
glbaligndiag.cpp
glbaligndiag.cpp
 
 
glbalignle.cpp
glbalignle.cpp
 
 
glbalignsimple.cpp
glbalignsimple.cpp
 
 
glbalignsp.cpp
glbalignsp.cpp
 
 
glbalignspn.cpp
glbalignspn.cpp
 
 
glbalignss.cpp
glbalignss.cpp
 
 
glbalndimer.cpp
glbalndimer.cpp
 
 
globals.cpp
globals.cpp
 
 
globalslinux.cpp
globalslinux.cpp
 
 
globalsosx.cpp
globalsosx.cpp
 
 
globalsother.cpp
globalsother.cpp
 
 
globalswin32.cpp
globalswin32.cpp
 
 
gonnet.cpp
gonnet.cpp
 
 
gonnet.h
gonnet.h
 
 
henikoffweight.cpp
henikoffweight.cpp
 
 
henikoffweightpb.cpp
henikoffweightpb.cpp
 
 
html.cpp
html.cpp
 
 
hydro.cpp
hydro.cpp
 
 
intmath.cpp
intmath.cpp
 
 
intmath.h
intmath.h
 
 
local.cpp
local.cpp
 
 
main.cpp
main.cpp
 
 
makerootmsa.cpp
makerootmsa.cpp
 
 
makerootmsab.cpp
makerootmsab.cpp
 
 
maketree.cpp
maketree.cpp
 
 
mhack.cpp
mhack.cpp
 
 
mpam200.cpp
mpam200.cpp
 
 
msa.cpp
msa.cpp
 
 
msa.h
msa.h
 
 
msa2.cpp
msa2.cpp
 
 
msadist.h
msadist.h
 
 
msadistkimura.cpp
msadistkimura.cpp
 
 
msadistkimura.h
msadistkimura.h
 
 
msadistmafft.h
msadistmafft.h
 
 
msf.cpp
msf.cpp
 
 
muscle.cpp
muscle.cpp
 
 

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Overview

MUSCLE Version 3.8.1551 July 12, 2014

http://www.drive5.com/muscle

This software is donated to the public domain.

Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

Modifications

3.8.1551.gsl3 Feb 11, 2020

  • Ported code to build natively on Windows in 64bit with MSVC.

3.8.1551.gsl2 Sep 27, 2018

  • Do not use -maxiters to abort pre-emptively due to incomplete "ptrBestMSA" results. Note: -maxhours will output the same incomplete results.

3.8.1551.gsl1 Aug 21, 2018

  • Exit after -maxiters and save results with chosen output format.

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Multiple Sequence Comparison by Log-Expectation.

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Windows 64bit Latest
Feb 11, 2020

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